6Z02

Photosynthetic Reaction Center From Rhodobacter Sphaeroides strain RV in surfo crystallization

PDB DOI: https://doi.org/10.2210/pdb6Z02/pdb

Classification: PHOTOSYNTHESIS
Organism(s): Cereibacter sphaeroides
Expression System: Cereibacter sphaeroides
Mutation(s): No
Membrane Protein: Yes PDBTMMemProtMDmpstruc

Deposited: 2020-05-07 Released: 2020-12-02
Deposition Author(s): Gabdulkhakov, A.G., Selikhanov, G.K., Fufina, T.Y., Vasilieva, L.G., Betzel, C.
Funding Organization(s): Russian Foundation for Basic Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.226
R-Value Work: 0.201
R-Value Observed: 0.203

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Novel approaches for the lipid sponge phase crystallization of the Rhodobacter sphaeroides photosynthetic reaction center.

Selikhanov, G., Fufina, T., Vasilieva, L., Betzel, C., Gabdulkhakov, A.

(2020) IUCrJ 7: 1084-1091

PubMed: 33209319 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1107/S2052252520012142
Primary Citation of Related Structures:
6Z02, 6Z1J, 6Z27

PubMed Abstract:
With the recent developments in the field of free-electron-laser-based serial femtosecond crystallography, the necessity to obtain a large number of high-quality crystals has emerged. In this work crystallization techniques were selected, tested and optimized for the lipid mesophase crystallization of the Rhodobacter sphaeroides membrane pigment-protein complex, known as the photosynthetic reaction center (RC). Novel approaches for lipid sponge phase crystallization in comparatively large volumes using Hamilton gas-tight glass syringes and plastic pipetting tips are described. An analysis of RC crystal structures obtained by lipid mesophase crystallization revealed non-native ligands that displaced the native electron-transfer cofactors (carotenoid sphero-idene and a ubi-quinone molecule) from their binding pockets. These ligands were identified and were found to be lipids that are major mesophase components. The selection of distinct co-crystallization conditions with the missing cofactors facilitated the restoration of sphero-idene in its binding site.

Organizational Affiliation

Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, Puschino, Moscow region 142290, Russian Federation.

Macromolecule Content

Total Structure Weight: 105.78 kDa
Atom Count: 7,930
Modelled Residue Count: 823
Deposited Residue Count: 824
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein H chain	A [auth H]	241	Cereibacter sphaeroides	Mutation(s): 0 Gene Names: puhA Membrane Entity: Yes
UniProt
Find proteins for P0C0Y7 (Cereibacter sphaeroides) Explore P0C0Y7 Go to UniProtKB: P0C0Y7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0C0Y7
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein L chain	B [auth L]	281	Cereibacter sphaeroides	Mutation(s): 0 Gene Names: pufL Membrane Entity: Yes
UniProt
Find proteins for P0C0Y8 (Cereibacter sphaeroides) Explore P0C0Y8 Go to UniProtKB: P0C0Y8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0C0Y8
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein M chain	C [auth M]	302	Cereibacter sphaeroides	Mutation(s): 0 Gene Names: pufM Membrane Entity: Yes
UniProt
Find proteins for P0C0Y9 (Cereibacter sphaeroides) Explore P0C0Y9 Go to UniProtKB: P0C0Y9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0C0Y9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 16 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL (Subject of Investigation/LOI) Query on CDL Download Ideal Coordinates CCD File SDF format, chain UA [auth M] MOL2 format, chain UA [auth M] mmCIF format, chain UA [auth M]	UA [auth M]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain UA [auth M] Interactions & Density Focus chain UA [auth M]
BCL (Subject of Investigation/LOI) Query on BCL Download Ideal Coordinates CCD File SDF format, chain HA [auth M] SDF format, chain IA [auth M] SDF format, chain R [auth L] SDF format, chain JA [auth M] MOL2 format, chain HA [auth M] MOL2 format, chain IA [auth M] MOL2 format, chain R [auth L] MOL2 format, chain JA [auth M] mmCIF format, chain HA [auth M] mmCIF format, chain IA [auth M] mmCIF format, chain R [auth L] mmCIF format, chain JA [auth M]	HA [auth M], IA [auth M], JA [auth M], R [auth L]	BACTERIOCHLOROPHYLL A C₅₅ H₇₄ Mg N₄ O₆ DSJXIQQMORJERS-AGGZHOMASA-M		Interactions Focus chain HA [auth M] Focus chain IA [auth M] Focus chain JA [auth M] Focus chain R [auth L] Interactions & Density Focus chain HA [auth M] Focus chain IA [auth M] Focus chain JA [auth M] Focus chain R [auth L]
BPH (Subject of Investigation/LOI) Query on BPH Download Ideal Coordinates CCD File SDF format, chain S [auth L] SDF format, chain KA [auth M] MOL2 format, chain S [auth L] MOL2 format, chain KA [auth M] mmCIF format, chain S [auth L] mmCIF format, chain KA [auth M]	KA [auth M], S [auth L]	BACTERIOPHEOPHYTIN A C₅₅ H₇₆ N₄ O₆ KWOZSBGNAHVCKG-SZQBJALDSA-N		Interactions Focus chain KA [auth M] Focus chain S [auth L] Interactions & Density Focus chain KA [auth M] Focus chain S [auth L]
U10 (Subject of Investigation/LOI) Query on U10 Download Ideal Coordinates CCD File SDF format, chain MA [auth M] SDF format, chain T [auth L] MOL2 format, chain MA [auth M] MOL2 format, chain T [auth L] mmCIF format, chain MA [auth M] mmCIF format, chain T [auth L]	MA [auth M], T [auth L]	UBIQUINONE-10 C₅₉ H₉₀ O₄ ACTIUHUUMQJHFO-UPTCCGCDSA-N		Interactions Focus chain MA [auth M] Focus chain T [auth L] Interactions & Density Focus chain MA [auth M] Focus chain T [auth L]
SPN (Subject of Investigation/LOI) Query on SPN Download Ideal Coordinates CCD File SDF format, chain NA [auth M] MOL2 format, chain NA [auth M] mmCIF format, chain NA [auth M]	NA [auth M]	SPEROIDENONE C₄₁ H₇₀ O₂ GWQAMGYOEYXWJF-YCDPMLDASA-N		Interactions Focus chain NA [auth M] Interactions & Density Focus chain NA [auth M]
LDA Query on LDA Download Ideal Coordinates CCD File SDF format, chain D [auth H] SDF format, chain E [auth H] SDF format, chain PA [auth M] SDF format, chain QA [auth M] SDF format, chain U [auth L] SDF format, chain AB [auth M] SDF format, chain OA [auth M] MOL2 format, chain D [auth H] MOL2 format, chain E [auth H] MOL2 format, chain PA [auth M] MOL2 format, chain QA [auth M] MOL2 format, chain U [auth L] MOL2 format, chain AB [auth M] MOL2 format, chain OA [auth M] mmCIF format, chain D [auth H] mmCIF format, chain E [auth H] mmCIF format, chain PA [auth M] mmCIF format, chain QA [auth M] mmCIF format, chain U [auth L] mmCIF format, chain AB [auth M] mmCIF format, chain OA [auth M]	AB [auth M] D [auth H] E [auth H] OA [auth M] PA [auth M] AB [auth M], D [auth H], E [auth H], OA [auth M], PA [auth M], QA [auth M], U [auth L]	LAURYL DIMETHYLAMINE-N-OXIDE C₁₄ H₃₁ N O SYELZBGXAIXKHU-UHFFFAOYSA-N		Interactions Focus chain AB [auth M] Focus chain D [auth H] Focus chain E [auth H] Focus chain OA [auth M] Focus chain PA [auth M] Focus chain QA [auth M] Focus chain U [auth L] Interactions & Density Focus chain AB [auth M] Focus chain D [auth H] Focus chain E [auth H] Focus chain OA [auth M] Focus chain PA [auth M] Focus chain QA [auth M] Focus chain U [auth L]
MYS Query on MYS Download Ideal Coordinates CCD File SDF format, chain I [auth H] SDF format, chain RA [auth M] SDF format, chain W [auth L] MOL2 format, chain I [auth H] MOL2 format, chain RA [auth M] MOL2 format, chain W [auth L] mmCIF format, chain I [auth H] mmCIF format, chain RA [auth M] mmCIF format, chain W [auth L]	I [auth H], RA [auth M], W [auth L]	PENTADECANE C₁₅ H₃₂ YCOZIPAWZNQLMR-UHFFFAOYSA-N		Interactions Focus chain I [auth H] Focus chain RA [auth M] Focus chain W [auth L] Interactions & Density Focus chain I [auth H] Focus chain RA [auth M] Focus chain W [auth L]
D12 Query on D12 Download Ideal Coordinates CCD File SDF format, chain F [auth H] SDF format, chain G [auth H] SDF format, chain SA [auth M] SDF format, chain TA [auth M] SDF format, chain V [auth L] SDF format, chain H MOL2 format, chain F [auth H] MOL2 format, chain G [auth H] MOL2 format, chain SA [auth M] MOL2 format, chain TA [auth M] MOL2 format, chain V [auth L] MOL2 format, chain H mmCIF format, chain F [auth H] mmCIF format, chain G [auth H] mmCIF format, chain SA [auth M] mmCIF format, chain TA [auth M] mmCIF format, chain V [auth L] mmCIF format, chain H	F [auth H] G [auth H] H SA [auth M] TA [auth M] F [auth H], G [auth H], H, SA [auth M], TA [auth M], V [auth L]	DODECANE C₁₂ H₂₆ SNRUBQQJIBEYMU-UHFFFAOYSA-N		Interactions Focus chain F [auth H] Focus chain G [auth H] Focus chain H Focus chain SA [auth M] Focus chain TA [auth M] Focus chain V [auth L] Interactions & Density Focus chain F [auth H] Focus chain G [auth H] Focus chain H Focus chain SA [auth M] Focus chain TA [auth M] Focus chain V [auth L]
HTO Query on HTO Download Ideal Coordinates CCD File SDF format, chain EA [auth L] SDF format, chain GA [auth L] SDF format, chain FA [auth L] MOL2 format, chain EA [auth L] MOL2 format, chain GA [auth L] MOL2 format, chain FA [auth L] mmCIF format, chain EA [auth L] mmCIF format, chain GA [auth L] mmCIF format, chain FA [auth L]	EA [auth L], FA [auth L], GA [auth L]	HEPTANE-1,2,3-TRIOL C₇ H₁₆ O₃ HXYCHJFUBNTKQR-RNFRBKRXSA-N		Interactions Focus chain EA [auth L] Focus chain FA [auth L] Focus chain GA [auth L] Interactions & Density Focus chain EA [auth L] Focus chain FA [auth L] Focus chain GA [auth L]
D10 Query on D10 Download Ideal Coordinates CCD File SDF format, chain X [auth L] MOL2 format, chain X [auth L] mmCIF format, chain X [auth L]	X [auth L]	DECANE C₁₀ H₂₂ DIOQZVSQGTUSAI-UHFFFAOYSA-N		Interactions Focus chain X [auth L] Interactions & Density Focus chain X [auth L]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain J [auth H] SDF format, chain VA [auth M] SDF format, chain WA [auth M] MOL2 format, chain J [auth H] MOL2 format, chain VA [auth M] MOL2 format, chain WA [auth M] mmCIF format, chain J [auth H] mmCIF format, chain VA [auth M] mmCIF format, chain WA [auth M]	J [auth H], VA [auth M], WA [auth M]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain J [auth H] Focus chain VA [auth M] Focus chain WA [auth M] Interactions & Density Focus chain J [auth H] Focus chain VA [auth M] Focus chain WA [auth M]
DIO Query on DIO Download Ideal Coordinates CCD File SDF format, chain Y [auth L] MOL2 format, chain Y [auth L] mmCIF format, chain Y [auth L]	Y [auth L]	1,4-DIETHYLENE DIOXIDE C₄ H₈ O₂ RYHBNJHYFVUHQT-UHFFFAOYSA-N		Interactions Focus chain Y [auth L] Interactions & Density Focus chain Y [auth L]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth L] SDF format, chain BA [auth L] SDF format, chain CA [auth L] SDF format, chain DA [auth L] SDF format, chain L [auth H] SDF format, chain M [auth H] SDF format, chain O [auth H] SDF format, chain XA [auth M] SDF format, chain YA [auth M] SDF format, chain Z [auth L] SDF format, chain ZA [auth M] SDF format, chain K [auth H] SDF format, chain N [auth H] MOL2 format, chain AA [auth L] MOL2 format, chain BA [auth L] MOL2 format, chain CA [auth L] MOL2 format, chain DA [auth L] MOL2 format, chain L [auth H] MOL2 format, chain M [auth H] MOL2 format, chain O [auth H] MOL2 format, chain XA [auth M] MOL2 format, chain YA [auth M] MOL2 format, chain Z [auth L] MOL2 format, chain ZA [auth M] MOL2 format, chain K [auth H] MOL2 format, chain N [auth H] mmCIF format, chain AA [auth L] mmCIF format, chain BA [auth L] mmCIF format, chain CA [auth L] mmCIF format, chain DA [auth L] mmCIF format, chain L [auth H] mmCIF format, chain M [auth H] mmCIF format, chain O [auth H] mmCIF format, chain XA [auth M] mmCIF format, chain YA [auth M] mmCIF format, chain Z [auth L] mmCIF format, chain ZA [auth M] mmCIF format, chain K [auth H] mmCIF format, chain N [auth H]	AA [auth L] BA [auth L] CA [auth L] DA [auth L] K [auth H] AA [auth L], BA [auth L], CA [auth L], DA [auth L], K [auth H], L [auth H], M [auth H], N [auth H], O [auth H], XA [auth M], YA [auth M], Z [auth L], ZA [auth M]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth L] Focus chain BA [auth L] Focus chain CA [auth L] Focus chain DA [auth L] Focus chain K [auth H] Focus chain L [auth H] Focus chain M [auth H] Focus chain N [auth H] Focus chain O [auth H] Focus chain XA [auth M] Focus chain YA [auth M] Focus chain Z [auth L] Focus chain ZA [auth M] Interactions & Density Focus chain AA [auth L] Focus chain BA [auth L] Focus chain CA [auth L] Focus chain DA [auth L] Focus chain K [auth H] Focus chain L [auth H] Focus chain M [auth H] Focus chain N [auth H] Focus chain O [auth H] Focus chain XA [auth M] Focus chain YA [auth M] Focus chain Z [auth L] Focus chain ZA [auth M]
FE (Subject of Investigation/LOI) Query on FE Download Ideal Coordinates CCD File SDF format, chain LA [auth M] MOL2 format, chain LA [auth M] mmCIF format, chain LA [auth M]	LA [auth M]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain LA [auth M] Interactions & Density Focus chain LA [auth M]
K Query on K Download Ideal Coordinates CCD File SDF format, chain Q [auth H] MOL2 format, chain Q [auth H] mmCIF format, chain Q [auth H]	Q [auth H]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain Q [auth H] Interactions & Density Focus chain Q [auth H]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain P [auth H] MOL2 format, chain P [auth H] mmCIF format, chain P [auth H]	P [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain P [auth H] Interactions & Density Focus chain P [auth H]