4RKU | pdb_00004rku

Crystal structure of plant Photosystem I at 3 Angstrom resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 
    0.293 (Depositor), 0.294 (DCC) 
  • R-Value Work: 
    0.258 (Depositor), 0.263 (DCC) 
  • R-Value Observed: 
    0.259 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history. 

Literature

Crystal structure of plant Photosystem I at 3.1 Angstrom resolution

Mazor, Y., Borovikova, A., Greenberg, I., Nelson, N.

To be published.

Macromolecule Content 

  • Total Structure Weight: 528.53 kDa 
  • Atom Count: 34,540 
  • Modeled Residue Count: 3,094 
  • Deposited Residue Count: 3,288 
  • Unique protein chains: 17

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1721Lathyrus oleraceusMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P05310 (Pisum sativum)
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2731Lathyrus oleraceusMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur center80Lathyrus oleraceusMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P10793 (Pisum sativum)
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit II, chloroplastic137Lathyrus oleraceusMutation(s): 0 
UniProt
Find proteins for E1C9K8 (Pisum sativum)
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IV B, chloroplastic63Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for E1C9K6 (Pisum sativum)
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit III, chloroplastic152Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A0H2UKZ4 (Pisum sativum)
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit V, chloroplastic84Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P20120 (Pisum sativum)
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VI, chloroplastic82Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for E1C9K9 (Pisum sativum)
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIII26Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P17227 (Pisum sativum)
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IX40Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D5MAL3 (Pisum sativum)
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit X psaK72Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for E1C9L3 (Pisum sativum)
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XI, chloroplastic163Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I-N subunitM [auth N]85Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for E1C9K7 (Pisum sativum)
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein 6A, chloroplasticN [auth 1]182Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for E1C9L2 (Pisum sativum)
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Type II chlorophyll a/b binding protein from photosystem IO [auth 2]199Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q41038 (Pisum sativum)
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Reference Sequence
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein 3, chloroplasticP [auth 3]275Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q32904 (Pisum sativum)
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Reference Sequence
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein P4, chloroplasticQ [auth 4]196Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9SQL2 (Pisum sativum)
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Reference Sequence

Small Molecules

Ligands 11 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD

Query on DGD


Download:Ideal Coordinates CCD File
XB [auth B]DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CL0

Query on CL0


Download:Ideal Coordinates CCD File
SB [auth A]CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
CLA

Query on CLA


Download:Ideal Coordinates CCD File
AA [auth A]
AB [auth A]
AD [auth B]
AE [auth G]
AF [auth 1]
AA [auth A],
AB [auth A],
AD [auth B],
AE [auth G],
AF [auth 1],
AG [auth 3],
AH [auth 4],
BA [auth A],
BB [auth A],
BD [auth B],
BE [auth G],
BF [auth 1],
BG [auth 3],
BH [auth 4],
CA [auth A],
CB [auth A],
CD [auth B],
CF [auth 1],
CG [auth 3],
CH [auth 4],
DA [auth A],
DB [auth A],
DD [auth B],
DF [auth 1],
DG [auth 3],
DH [auth 4],
EA [auth A],
EB [auth A],
EC [auth B],
ED [auth B],
EE [auth H],
EF [auth 1],
EG [auth 3],
EH [auth 4],
FA [auth A],
FB [auth A],
FC [auth B],
FD [auth B],
FF [auth 1],
FG [auth 3],
GA [auth A],
GB [auth A],
GC [auth B],
GD [auth B],
GF [auth 1],
GG [auth 3],
HA [auth A],
HB [auth A],
HC [auth B],
HD [auth B],
HF [auth 1],
HG [auth 3],
IA [auth A],
IB [auth A],
IC [auth B],
ID [auth B],
IG [auth 3],
JA [auth A],
JB [auth A],
JC [auth B],
JD [auth B],
JF [auth 2],
JG [auth 3],
KA [auth A],
KB [auth A],
KC [auth B],
KD [auth B],
KE [auth J],
KF [auth 2],
KG [auth 3],
LA [auth A],
LB [auth A],
LC [auth B],
LD [auth B],
LE [auth J],
LF [auth 2],
LG [auth 3],
MA [auth A],
MB [auth A],
MC [auth B],
MD [auth B],
ME [auth J],
MF [auth 2],
MG [auth 3],
NA [auth A],
NB [auth A],
NC [auth B],
ND [auth B],
NF [auth 2],
NG [auth 3],
OA [auth A],
OB [auth A],
OC [auth B],
OD [auth B],
OF [auth 2],
OG [auth 3],
PA [auth A],
PB [auth A],
PC [auth B],
PD [auth B],
PE [auth L],
PF [auth 2],
PG [auth 3],
QA [auth A],
QB [auth A],
QC [auth B],
QD [auth B],
QE [auth L],
QF [auth 2],
QG [auth 4],
RA [auth A],
RC [auth B],
RD [auth B],
RE [auth L],
RF [auth 2],
RG [auth 4],
SA [auth A],
SC [auth B],
SD [auth B],
SF [auth 2],
SG [auth 4],
TA [auth A],
TB [auth A],
TC [auth B],
TF [auth 2],
TG [auth 4],
UA [auth A],
UB [auth A],
UC [auth B],
UE [auth 1],
UF [auth 2],
UG [auth 4],
VA [auth A],
VC [auth B],
VE [auth 1],
VF [auth 2],
VG [auth 4],
WA [auth A],
WC [auth B],
WE [auth 1],
WF [auth 2],
WG [auth 4],
XA [auth A],
XC [auth B],
XD [auth F],
XE [auth 1],
XG [auth 4],
YA [auth A],
YC [auth B],
YD [auth F],
YE [auth 1],
YG [auth 4],
ZA [auth A],
ZC [auth B],
ZD [auth F],
ZE [auth 1],
ZG [auth 4]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
LMG

Query on LMG


Download:Ideal Coordinates CCD File
DE [auth G],
JE [auth J]		1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG

Query on LHG


Download:Ideal Coordinates CCD File
IF [auth 1],
WB [auth B],
Y [auth A],
Z [auth A],
ZF [auth 2]		1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
NEX

Query on NEX


Download:Ideal Coordinates CCD File
HH [auth 4](1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL
C40 H56 O4
PGYAYSRVSAJXTE-OQASCVKESA-N
LUT

Query on LUT


Download:Ideal Coordinates CCD File
FH [auth 4]
GH [auth 4]
SE [auth 1]
TE [auth 1]
XF [auth 2]
FH [auth 4],
GH [auth 4],
SE [auth 1],
TE [auth 1],
XF [auth 2],
YF [auth 2]
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O2
KBPHJBAIARWVSC-NSIPBSJQSA-N
BCR

Query on BCR


Download:Ideal Coordinates CCD File
AC [auth B]
BC [auth B]
CC [auth B]
CE [auth G]
DC [auth B]
AC [auth B],
BC [auth B],
CC [auth B],
CE [auth G],
DC [auth B],
FE [auth I],
GE [auth I],
HE [auth J],
IE [auth J],
NE [auth L],
OE [auth L],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
VD [auth F],
W [auth A],
WD [auth F],
X [auth A],
YB [auth B],
ZB [auth B]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
PQN

Query on PQN


Download:Ideal Coordinates CCD File
R [auth A],
VB [auth B]		PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4

Query on SF4


Download:Ideal Coordinates CCD File
RB [auth A],
TD [auth C],
UD [auth C]		IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
G3P

Query on G3P


Download:Ideal Coordinates CCD File
IH [auth 4]SN-GLYCEROL-3-PHOSPHATE
C3 H9 O6 P
AWUCVROLDVIAJX-GSVOUGTGSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free:  0.293 (Depositor), 0.294 (DCC) 
  • R-Value Work:  0.258 (Depositor), 0.263 (DCC) 
  • R-Value Observed: 0.259 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.631α = 90
b = 189.168β = 91.11
c = 129.667γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
MOLREPphasing
PHENIXrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-04
    Type: Initial release
  • Version 2.0: 2024-11-06
    Changes: Advisory, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary