6YX8

The structure of allophycocyanin from cyanobacterium Nostoc sp. WR13, the C2221 crystal form.

• PDB DOI: https://doi.org/10.2210/pdb6YX8/pdb

• Classification: PHOTOSYNTHESIS
• Organism(s): Nostoc sp. WR13
• Mutation(s): No 


• Deposited: 2020-04-30 Released: 2021-05-12 
• Deposition Author(s): Patel, H.M., Roszak, A.W., Madamwar, D., Cogdell, R.J.
• Funding Organization(s): Department of Energy (DOE, United States), Department of Biotechnology (DBT, India)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 0.198 
• R-Value Work: 0.160 

Starting Model: experimental

Literature

The high resolution structure of allophycocyanin from cyanobacterium Nostoc sp. WR13

Patel, H.M., Roszak, A.W., Madamwar, D., Cogdell, R.J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A3B3 Pseudo Symmetry: Cyclic - C3  (Explore in 3D)
Pseudo Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 116.82 kDa 
• Atom Count: 9,412 
• Modelled Residue Count: 963 
• Deposited Residue Count: 963 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALPHA SUBUNIT OF CYANOBACTERIAL ALLOPHYCOCYANIN PROTEIN	A [auth AAA], C [auth CCC], E [auth EEE]	160	Nostoc sp. WR13	Mutation(s): 0
UniProt
Find proteins for A0A4Y5PW22 (Nostoc sp. WR13) Explore A0A4Y5PW22  Go to UniProtKB:  A0A4Y5PW22

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA SUBUNIT OF CYANOBACTERIAL ALLOPHYCOCYANIN PROTEIN	B [auth BBB], D [auth DDD], F [auth FFF]	161	Nostoc sp. WR13	Mutation(s): 0
UniProt
Find proteins for A0A4Y5PW23 (Nostoc sp. WR13) Explore A0A4Y5PW23  Go to UniProtKB:  A0A4Y5PW23

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PXQ (Subject of Investigation/LOI)	G [auth AAA], JC [auth FFF], OA [auth CCC], RB [auth EEE], W [auth BBB], ZA [auth DDD]	3-[5-[[(3~{R},4~{R})-3-ethyl-4-methyl-5-oxidanylidene-3,4-dihydropyrrol-2-yl]methyl]-2-[[5-[(~{Z})-(4-ethyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1~{H}-pyrrol-2-yl]methyl]-4-methyl-1~{H}-pyrrol-3-yl]propanoic acid C33 H42 N4 O6 RIXXCMVADHNPLY-UKJJQICTSA-N
1PE	AA [auth BBB], BA [auth BBB], J [auth AAA], MA [auth BBB], OC [auth FFF]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
PG4	EB [auth DDD], FB [auth DDD], GB [auth DDD], QB [auth EEE], TB [auth EEE]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
BCN	DB [auth DDD], I [auth AAA]	BICINE C6 H13 N O4 FSVCELGFZIQNCK-UHFFFAOYSA-N
PGE	CA [auth BBB], DA [auth BBB], IC [auth EEE], K [auth AAA], PC [auth FFF], QA [auth CCC], QC [auth FFF], RC [auth FFF], SC [auth FFF], U [auth AAA], UB [auth EEE]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
MRD	SB [auth EEE]	(4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N
MPD	AB [auth DDD], BB [auth DDD], CB [auth DDD], H [auth AAA], KC [auth FFF], LC [auth FFF], MC [auth FFF], NC [auth FFF], PA [auth CCC], X [auth BBB], Y [auth BBB], Z [auth BBB]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
PEG	EA [auth BBB], FA [auth BBB], GA [auth BBB], HB [auth DDD], IB [auth DDD], JB [auth DDD], L [auth AAA], M [auth AAA], N [auth AAA], O [auth AAA], RA [auth CCC], SA [auth CCC], TA [auth CCC], TC [auth FFF], UA [auth CCC], UC [auth FFF], VB [auth EEE], VC [auth FFF], WB [auth EEE], WC [auth FFF], XA [auth CCC], XB [auth EEE], YB [auth EEE]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	AC [auth EEE], AD [auth FFF], BC [auth EEE], CC [auth EEE], DC [auth EEE], EC [auth EEE], FC [auth EEE], GC [auth EEE], HA [auth BBB], HC [auth EEE], IA [auth BBB], JA [auth BBB], KA [auth BBB], KB [auth DDD], LA [auth BBB], LB [auth DDD], MB [auth DDD], NA [auth CCC], NB [auth DDD], OB [auth DDD], P [auth AAA], PB [auth DDD], Q [auth AAA], R [auth AAA], S [auth AAA], T [auth AAA], V [auth AAA], VA [auth CCC], WA [auth CCC], XC [auth FFF], YA [auth DDD], YC [auth FFF], ZB [auth EEE], ZC [auth FFF]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MEN	B [auth BBB], D [auth DDD], F [auth FFF]	L-PEPTIDE LINKING	C5 H10 N2 O3		ASN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 0.198 
• R-Value Work: 0.160 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.676	α = 90
b = 177.34	β = 90
c = 122.416	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
autoPROC	data scaling
STARANISO	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-05-12 
Deposition Author(s): Patel, H.M., Roszak, A.W., Madamwar, D., Cogdell, R.J.

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Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	DE-SC0001035 (Office of Basic Energy Sciences)
Department of Biotechnology (DBT, India)	India	BT/PR15686/AAQ/3/811/2016 (UGC-BSR Faculty Fellowship)
Department of Biotechnology (DBT, India)	India	BT/IN/UK/DBT-BC/2017-18 (Newton-Bhabha fellowship)

Revision History  

• Version 1.0: 2021-05-12
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description