6ZXS

Cold grown Pea Photosystem I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.240 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 5L8R


Literature

Structure of cold grown pea Photosystem I

Nelson, N.Caspy, I.Subramanyam, R.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1743Pisum sativumMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2733Pisum sativumMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for A0A0F6NGI2 (Pisum sativum)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur center80Pisum sativumMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P10793 (Pisum sativum)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
PsaD143Pisum sativumMutation(s): 0 
UniProt
Find proteins for E1C9K8 (Pisum sativum)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
PsaE66Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for E1C9K6 (Pisum sativum)
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UniProt GroupE1C9K6
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit III154Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A0M3KL12 (Pisum sativum)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
PsaG97Pisum sativumMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VI88Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A0M3KL10 (Pisum sativum)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIII30Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P17227 (Pisum sativum)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IX42Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D5MAL3 (Pisum sativum)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit X psaK80Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for E1C9L3 (Pisum sativum)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
PsaL domain-containing protein157Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Lhca1M [auth 1]193Pisum sativumMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticN [auth 2]208Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q41038 (Pisum sativum)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein 3, chloroplasticO [auth 3]221Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q32904 (Pisum sativum)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein P4, chloroplasticP [auth 4]198Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9SQL2 (Pisum sativum)
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Small Molecules
Ligands 15 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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HH [auth 2],
IE [auth F],
OF [auth 1],
VD [auth B],
ZE [auth J]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL
Query on CHL

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AG [auth 1]
CG [auth 1]
CI [auth 4]
NI [auth 4]
OI [auth 4]
AG [auth 1],
CG [auth 1],
CI [auth 4],
NI [auth 4],
OI [auth 4],
QI [auth 4],
RH [auth 3],
RI [auth 4],
SI [auth 4],
TH [auth 3],
UG [auth 2],
UH [auth 3],
VG [auth 2],
WG [auth 2],
XH [auth 3],
YG [auth 2],
ZG [auth 2]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CLA
Query on CLA

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AA [auth A]
AB [auth A]
AC [auth B]
AD [auth B]
AE [auth F]
AA [auth A],
AB [auth A],
AC [auth B],
AD [auth B],
AE [auth F],
AI [auth 3],
BA [auth A],
BB [auth A],
BC [auth B],
BD [auth B],
BE [auth F],
BF [auth K],
BG [auth 1],
CA [auth A],
CB [auth A],
CC [auth B],
CD [auth B],
CE [auth F],
CF [auth K],
DA [auth A],
DB [auth A],
DC [auth B],
DD [auth B],
DF [auth K],
DG [auth 1],
EA [auth A],
EC [auth B],
ED [auth B],
EF [auth K],
EG [auth 1],
FA [auth A],
FC [auth B],
FD [auth B],
FI [auth 4],
GA [auth A],
GC [auth B],
GD [auth B],
GF [auth L],
GH [auth 2],
GI [auth 4],
HA [auth A],
HC [auth B],
HD [auth B],
HI [auth 4],
IA [auth A],
IC [auth B],
IH [auth 3],
II [auth 4],
JA [auth A],
JC [auth B],
JF [auth L],
JI [auth 4],
KA [auth A],
KC [auth B],
KE [auth G],
KF [auth L],
KI [auth 4],
LA [auth A],
LC [auth B],
LE [auth G],
LF [auth L],
LI [auth 4],
MA [auth A],
MC [auth B],
ME [auth G],
MG [auth 2],
MI [auth 4],
NA [auth A],
NC [auth B],
NG [auth 2],
OA [auth A],
OC [auth B],
OG [auth 2],
OH [auth 3],
PA [auth A],
PB [auth A],
PC [auth B],
PG [auth 2],
PH [auth 3],
PI [auth 4],
QA [auth A],
QB [auth A],
QC [auth B],
QG [auth 2],
QH [auth 3],
R [auth A],
RA [auth A],
RC [auth B],
RE [auth H],
RG [auth 2],
S [auth A],
SA [auth A],
SC [auth B],
SF [auth 1],
SG [auth 2],
SH [auth 3],
T [auth A],
TA [auth A],
TB [auth B],
TC [auth B],
TF [auth 1],
TG [auth 2],
U [auth A],
UA [auth A],
UC [auth B],
UE [auth J],
UF [auth 1],
V [auth A],
VA [auth A],
VB [auth B],
VC [auth B],
VF [auth 1],
VH [auth 3],
W [auth A],
WA [auth A],
WB [auth B],
WC [auth B],
WE [auth J],
WF [auth 1],
WH [auth 3],
X [auth A],
XA [auth A],
XB [auth B],
XC [auth B],
XF [auth 1],
XG [auth 2],
Y [auth A],
YA [auth A],
YB [auth B],
YC [auth B],
YF [auth 1],
YH [auth 3],
Z [auth A],
ZA [auth A],
ZB [auth B],
ZC [auth B],
ZF [auth 1],
ZH [auth 3]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
CL0
Query on CL0

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Q [auth A]CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
LMG
Query on LMG

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BH [auth 2]
CH [auth 2]
DH [auth 2]
EH [auth 2]
FE [auth F]
BH [auth 2],
CH [auth 2],
DH [auth 2],
EH [auth 2],
FE [auth F],
GE [auth F],
GG [auth 1],
HE [auth F],
HG [auth 2],
IG [auth 2],
NF [auth 1],
OB [auth A],
QD [auth B],
QE [auth G],
RD [auth B],
UD [auth B],
UI [auth 4],
VE [auth J]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
Query on LHG

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AH [auth 2]
FG [auth 1]
LB [auth A]
MB [auth A]
OD [auth B]
AH [auth 2],
FG [auth 1],
LB [auth A],
MB [auth A],
OD [auth B],
PD [auth B]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
XAT
Query on XAT

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EI [auth 4],
KG [auth 2]
(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O4
SZCBXWMUOPQSOX-WVJDLNGLSA-N
LUT
Query on LUT

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DI [auth 4]
JG [auth 2]
KH [auth 3]
LH [auth 3]
PF [auth 1]
DI [auth 4],
JG [auth 2],
KH [auth 3],
LH [auth 3],
PF [auth 1],
QF [auth 1],
YE [auth J]
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O2
KBPHJBAIARWVSC-NSIPBSJQSA-N
ZEX
Query on ZEX

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JE [auth F](1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol
C40 H56 O2
YRMDXLDAZBQLBK-WIHRHFSMSA-N
BCR
Query on BCR

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BI [auth 4]
DE [auth F]
EE [auth F]
FF [auth K]
GB [auth A]
BI [auth 4],
DE [auth F],
EE [auth F],
FF [auth K],
GB [auth A],
HB [auth A],
HF [auth L],
IB [auth A],
IF [auth L],
JB [auth A],
JD [auth B],
KB [auth A],
KD [auth B],
LD [auth B],
LG [auth 2],
MD [auth B],
MF [auth L],
MH [auth 3],
ND [auth B],
NE [auth G],
NH [auth 3],
RF [auth 1],
SB [auth A],
SE [auth I],
TE [auth I],
UB [auth B],
XE [auth J]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
Query on LMT

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AF [auth J]
FH [auth 2]
NB [auth A]
OE [auth G]
PE [auth G]
AF [auth J],
FH [auth 2],
NB [auth A],
OE [auth G],
PE [auth G],
SD [auth B],
TD [auth B],
TI [auth 4],
WD [auth B]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
PQN
Query on PQN

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EB [auth A],
ID [auth B]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4
Query on SF4

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FB [auth A],
YD [auth C],
ZD [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
GOL
Query on GOL

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RB [auth A],
VI [auth 4]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA
Query on CA

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JH [auth 3],
XD [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.240 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 190.197α = 90
b = 201.786β = 90
c = 213.614γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Israel Science FoundationIsrael569/17
The University Grants Committee, Research Grants Council (RGC)India2716/17

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-07
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Database references, Refinement description