7AP5 | pdb_00007ap5

Crystal structure of phycoerythrin from cyanobacterium Nostoc sp. WR13 contains multiple stacks of hexameric assemblies which resemble the rods of phycobilisome.

• PDB DOI: https://doi.org/10.2210/pdb7AP5/pdb

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


• Deposited: 2020-10-15 Released: 2021-11-17 
• Deposition Author(s): Patel, H.M., Roszak, A.W., Cogdell, R.J., Madamwar, D., Liu, H., Gross, M.L., Blankenship, R.E.
• 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: 2.13 Å
• R-Value Free: 
  0.225 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.190 (DCC) 

Starting Model: experimental

Literature

The crystal stacks of hexameric assemblies of phycoerythrin from cyanobacterium Nostoc sp. WR13 resemble rods of phycobilisome

Patel, H.M., Roszak, A.W., Liu, H., Gross, M.L., Blankenship, R.E., Madamwar, D., Cogdell, R.J.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Hetero 48-mer - A24B24 Pseudo Symmetry: Dihedral - D3  (Explore in 3D)
Pseudo Stoichiometry: Homo 48-mer - A48 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 355.85 kDa 
• Atom Count: 26,483 
• Modelled Residue Count: 2,784 
• Deposited Residue Count: 2,784 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha subunit of cyanobacterial protein phycoerythrin	A [auth AAA], C [auth CCC], E [auth EEE], G [auth GGG], I [auth III], K [auth KKK], M [auth MMM], O [auth OOO]	164	Nostoc sp. WR13	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta subunit of cyanobacterial protein phycoerythrin	B [auth BBB], D [auth DDD], F [auth FFF], H [auth HHH], J [auth JJJ], L [auth LLL], N [auth NNN], P [auth PPP]	184	Nostoc sp. WR13	Mutation(s): 0

Small Molecules

Ligands 13 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEB (Subject of Investigation/LOI)	AC [auth DDD], AD [auth EEE], AH [auth JJJ], BC [auth DDD], BD [auth EEE], EB [auth CCC], EF [auth HHH], FB [auth CCC], FF [auth HHH], FG [auth III], GF [auth HHH], GG [auth III], GL [auth PPP], HA [auth BBB], HL [auth PPP], IA [auth BBB], IL [auth PPP], JA [auth BBB], JI [auth LLL], JJ [auth MMM], KI [auth LLL], KJ [auth MMM], LI [auth LLL], ME [auth GGG], NE [auth GGG], Q [auth AAA], QD [auth FFF], R [auth AAA], RD [auth FFF], SD [auth FFF], SH [auth KKK], TH [auth KKK], TK [auth OOO], UK [auth OOO], XJ [auth NNN], YG [auth JJJ], YJ [auth NNN], ZB [auth DDD], ZG [auth JJJ], ZJ [auth NNN]	PHYCOERYTHROBILIN C33 H40 N4 O6 NKCBCVIFPXGHAV-WAVSMFBNSA-N
RWB	KA [auth BBB], MI [auth LLL]	dodecaethylene glycol monomethyl ether C25 H52 O13 PLQZJIIDLZRWBG-UHFFFAOYSA-N
PE5	AK [auth NNN]	3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL C18 H38 O9 CUDPPTPIUWYGFI-UHFFFAOYSA-N
PE8	LA [auth BBB]	3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL C16 H34 O9 GLZWNFNQMJAZGY-UHFFFAOYSA-N
P33	BH [auth JJJ], CC [auth DDD], DC [auth DDD], HF [auth HHH], IF [auth HHH], TD [auth FFF]	3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL C14 H30 O8 XPJRQAIZZQMSCM-UHFFFAOYSA-N
P6G	EC [auth DDD]	HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N
1PE	CD [auth EEE], CH [auth JJJ], DF [auth HHH], DH [auth JJJ], FC [auth DDD], JL [auth PPP], MA [auth BBB], NA [auth BBB], ND [auth FFF], NI [auth LLL], OA [auth BBB], XG [auth JJJ]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
PG4	BK [auth NNN], CK [auth NNN], DK [auth NNN], EH [auth JJJ], GB [auth CCC], GC [auth DDD], HC [auth DDD], JF [auth HHH], KF [auth HHH], KL [auth PPP], LJ [auth MMM], LL [auth PPP], MJ [auth MMM], NJ [auth MMM], OD [auth FFF], OE [auth GGG], OI [auth LLL], PE [auth GGG], PI [auth LLL], QE [auth GGG], QI [auth LLL], S [auth AAA], T [auth AAA], U [auth AAA], UD [auth FFF], UH [auth KKK], UJ [auth MMM], VD [auth FFF], VH [auth KKK], VJ [auth NNN], VK [auth OOO], WD [auth FFF], WH [auth KKK], WJ [auth NNN]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE	AA [auth AAA], CB [auth BBB], CF [auth GGG], DD [auth EEE], DG [auth HHH], ED [auth EEE], EK [auth NNN], FD [auth EEE], FH [auth JJJ], FK [auth NNN], GD [auth EEE], GH [auth JJJ], GK [auth NNN], HB [auth CCC], HG [auth III], HJ [auth LLL], HK [auth NNN], IB [auth CCC], IC [auth DDD], IG [auth III], IJ [auth LLL], JB [auth CCC], JC [auth DDD], JG [auth III], KB [auth CCC], KC [auth DDD], KG [auth III], LB [auth CCC], LF [auth HHH], MF [auth HHH], ML [auth PPP], NF [auth HHH], OF [auth HHH], OJ [auth MMM], PA [auth BBB], PF [auth HHH], PJ [auth MMM], QA [auth BBB], RE [auth GGG], RI [auth LLL], SE [auth GGG], SI [auth LLL], TE [auth GGG], V [auth AAA], W [auth AAA], WG [auth JJJ], WK [auth OOO], X [auth AAA], XD [auth FFF], XH [auth KKK], XK [auth OOO], Y [auth AAA], YD [auth FFF], YH [auth KKK], YK [auth OOO], Z [auth AAA], ZD [auth FFF]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	AE [auth FFF], AI [auth KKK], AJ [auth LLL], AL [auth OOO], BA [auth AAA], BE [auth FFF], BI [auth KKK], BL [auth OOO], CA [auth AAA], CE [auth FFF], CI [auth KKK], CL [auth OOO], DB [auth BBB], DE [auth FFF], DI [auth KKK], EE [auth FFF], EG [auth III], FL [auth PPP], HH [auth JJJ], IH [auth JJJ], IK [auth NNN], JH [auth JJJ], JK [auth NNN], KK [auth NNN], LC [auth DDD], LD [auth EEE], LG [auth III], MB [auth CCC], MC [auth DDD], MD [auth EEE], MG [auth III], NB [auth CCC], NC [auth DDD], NG [auth III], NL [auth PPP], OB [auth CCC], OC [auth DDD], OG [auth III], OL [auth PPP], PB [auth CCC], PG [auth III], PL [auth PPP], QB [auth CCC], QF [auth HHH], QJ [auth MMM], QL [auth PPP], RA [auth BBB], RB [auth CCC], RF [auth HHH], RJ [auth MMM], RL [auth PPP], SA [auth BBB], SB [auth CCC], SF [auth HHH], SJ [auth MMM], SL [auth PPP], TA [auth BBB], TF [auth HHH], TI [auth LLL], UA [auth BBB], UE [auth GGG], UF [auth HHH], UI [auth LLL], VA [auth BBB], VE [auth GGG], VI [auth LLL], WA [auth BBB], WB [auth CCC], WE [auth GGG], WI [auth LLL], XE [auth GGG], XI [auth LLL], YB [auth CCC], YE [auth GGG], YI [auth LLL], ZC [auth DDD], ZH [auth KKK], ZI [auth LLL], ZK [auth OOO]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4	AB [auth BBB], AF [auth GGG], AG [auth HHH], CJ [auth LLL], DA [auth AAA], DJ [auth LLL], DL [auth OOO], EA [auth AAA], EI [auth KKK], FI [auth KKK], GE [auth FFF], GI [auth KKK], HE [auth FFF], IE [auth FFF], JE [auth FFF], KE [auth FFF], KH [auth JJJ], LH [auth JJJ], MH [auth JJJ], NH [auth JJJ], OH [auth JJJ], OK [auth NNN], PK [auth NNN], QH [auth JJJ], QK [auth NNN], RC [auth DDD], RG [auth III], RK [auth NNN], SC [auth DDD], SG [auth III], SK [auth NNN], TB [auth CCC], TC [auth DDD], TG [auth III], UB [auth CCC], UC [auth DDD], UL [auth PPP], VC [auth DDD], VL [auth PPP], WC [auth DDD], WL [auth PPP], XA [auth BBB], XB [auth CCC], XF [auth HHH], YA [auth BBB], YF [auth HHH], ZA [auth BBB], ZE [auth GGG], ZF [auth HHH]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO	BJ [auth LLL], FE [auth FFF], HD [auth EEE], ID [auth EEE], LK [auth NNN], MK [auth NNN], NK [auth NNN], PC [auth DDD], PD [auth FFF], QC [auth DDD], QG [auth III], TL [auth PPP], UG [auth III], VF [auth HHH], WF [auth HHH]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NO3	BB [auth BBB], BF [auth GGG], BG [auth HHH], CG [auth HHH], EJ [auth LLL], EL [auth OOO], FA [auth AAA], FJ [auth LLL], GA [auth AAA], GJ [auth LLL], HI [auth KKK], II [auth KKK], JD [auth EEE], KD [auth EEE], LE [auth FFF], PH [auth JJJ], RH [auth JJJ], TJ [auth MMM], VB [auth CCC], VG [auth III], XC [auth DDD], XL [auth PPP], YC [auth DDD]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MEN	B [auth BBB], D [auth DDD], F [auth FFF], H [auth HHH], J [auth JJJ], L [auth LLL], N [auth NNN], P [auth PPP]	L-PEPTIDE LINKING	C5 H10 N2 O3		ASN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free:  0.225 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.190 (DCC) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 192.759	α = 90
b = 192.759	β = 90
c = 524.486	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data processing
pointless	data scaling
Aimless	data scaling
STARANISO	data scaling
PHASER	phasing
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-11-17 
Deposition Author(s): Patel, H.M., Roszak, A.W., Cogdell, R.J., Madamwar, D., Liu, H., Gross, M.L., Blankenship, R.E.

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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: 2021-11-17
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Derived calculations, Refinement description