6ZXS

Cold grown Pea Photosystem I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 
    0.270 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.239 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 
    0.240 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted DGDClick on this verticalbar to view detailsBest fitted CHLClick on this verticalbar to view detailsBest fitted CLAClick on this verticalbar to view detailsBest fitted CL0Click on this verticalbar to view detailsBest fitted LMGClick on this verticalbar to view detailsBest fitted LHGClick on this verticalbar to view detailsBest fitted XATClick on this verticalbar to view detailsBest fitted LUTClick on this verticalbar to view detailsBest fitted ZEXClick on this verticalbar to view detailsBest fitted BCRClick on this verticalbar to view detailsBest fitted LMTClick on this verticalbar to view detailsBest fitted PQNClick on this verticalbar to view details

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
Find proteins for A0A0F6NFW5 (Pisum sativum)
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UniProt GroupA0A0F6NFW5
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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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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
Find proteins for E1C9L1 (Pisum sativum)
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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 
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]
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]
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]
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]
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]
(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]
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]
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 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.239 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 0.240 (Depositor) 
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

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted DGDClick on this verticalbar to view detailsBest fitted CHLClick on this verticalbar to view detailsBest fitted CLAClick on this verticalbar to view detailsBest fitted CL0Click on this verticalbar to view detailsBest fitted LMGClick on this verticalbar to view detailsBest fitted LHGClick on this verticalbar to view detailsBest fitted XATClick on this verticalbar to view detailsBest fitted LUTClick on this verticalbar to view detailsBest fitted ZEXClick on this verticalbar to view detailsBest fitted BCRClick on this verticalbar to view detailsBest fitted LMTClick on this verticalbar to view detailsBest fitted PQNClick on this verticalbar to view details

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