3A0H

Crystal structure of I-substituted Photosystem II complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 0.326 
  • R-Value Work: 0.290 
  • R-Value Observed: 0.290 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Location of chloride and its possible functions in oxygen-evolving photosystem II revealed by X-ray crystallography

Kawakami, K.Umena, Y.Kamiya, N.Shen, J.-R.

(2009) Proc Natl Acad Sci U S A 106: 8567-8572

  • DOI: 10.1073/pnas.0812797106
  • Primary Citation of Related Structures:  
    3A0B, 3A0H

  • PubMed Abstract: 
  • The chloride ion, Cl(-), is an essential cofactor for oxygen evolution of photosystem II (PSII) and is closely associated with the Mn(4)Ca cluster. Its detailed location and function have not been identified, however. We substituted Cl(-) with a bromide ion (Br(-)) or an iodide ion (I(-)) in PSII and analyzed the crystal structures of PSII with Br(-) and I(-) substitutions ...

    The chloride ion, Cl(-), is an essential cofactor for oxygen evolution of photosystem II (PSII) and is closely associated with the Mn(4)Ca cluster. Its detailed location and function have not been identified, however. We substituted Cl(-) with a bromide ion (Br(-)) or an iodide ion (I(-)) in PSII and analyzed the crystal structures of PSII with Br(-) and I(-) substitutions. Substitution of Cl(-) with Br(-) did not inhibit oxygen evolution, whereas substitution of Cl(-) with I(-) completely inhibited oxygen evolution, indicating the efficient replacement of Cl(-) by I(-). PSII with Br(-) and I(-) substitutions were crystallized, and their structures were analyzed. The results showed that there are 2 anion-binding sites in each PSII monomer; they are located on 2 sides of the Mn(4)Ca cluster at equal distances from the metal cluster. Anion-binding site 1 is close to the main chain of D1-Glu-333, and site 2 is close to the main chain of CP43-Glu-354; these 2 residues are coordinated directly with the Mn(4)Ca cluster. In addition, site 1 is located in the entrance of a proton exit channel. These results indicate that these 2 Cl(-) anions are required to maintain the coordination structure of the Mn(4)Ca cluster as well as the proposed proton channel, thereby keeping the oxygen-evolving complex fully active.


    Organizational Affiliation

    Division of Bioscience, Graduate School of Natural Science and Technology/Faculty of Science; Okayama University, Okayama 700-8530, Japan.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem Q(B) proteinA,
U [auth a]
344Thermostichus vulcanusMutation(s): 0 
Gene Names: psbApsbA-1
EC: 1.10.3.9
Membrane Entity: Yes 
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UniProt GroupP51765
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II core light harvesting proteinB,
V [auth b]
488Thermostichus vulcanusMutation(s): 0 
Gene Names: psbB
Membrane Entity: Yes 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II CP43 proteinC,
W [auth c]
447Thermostichus vulcanusMutation(s): 0 
Gene Names: psbC
Membrane Entity: Yes 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II D2 proteinD,
X [auth d]
340Thermostichus vulcanusMutation(s): 0 
Gene Names: psbD
EC: 1.10.3.9
Membrane Entity: Yes 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaE,
Y [auth e]
83Thermostichus vulcanusMutation(s): 0 
Gene Names: psbE
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaF,
Z [auth f]
44Thermostichus vulcanusMutation(s): 0 
Gene Names: psbF
Membrane Entity: Yes 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein HG [auth H],
AA [auth h]
64Thermostichus vulcanusMutation(s): 0 
Gene Names: psbH
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein IH [auth I],
BA [auth i]
35Thermostichus vulcanusMutation(s): 0 
Gene Names: psbI
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein JI [auth J],
CA [auth j]
40Thermostichus vulcanusMutation(s): 0 
Gene Names: psbJ
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein KJ [auth K],
DA [auth k]
36Thermostichus vulcanusMutation(s): 0 
Gene Names: psbK
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein LK [auth L],
EA [auth l]
37Thermostichus vulcanusMutation(s): 0 
Gene Names: psbL
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein ML [auth M],
FA [auth m]
36Thermostichus vulcanusMutation(s): 0 
Gene Names: psbM
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II manganese-stabilizing polypeptideM [auth O],
GA [auth o]
242Thermostichus vulcanusMutation(s): 0 
Gene Names: psbO
Membrane Entity: Yes 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein TN [auth T],
HA [auth t]
30Thermostichus vulcanusMutation(s): 0 
Gene Names: psbT
Membrane Entity: Yes 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II 12 kDa extrinsic proteinO [auth U],
IA [auth u]
98Thermostichus vulcanusMutation(s): 0 
Gene Names: psbU
Membrane Entity: Yes 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c-550P [auth V],
JA [auth v]
137Thermostichus vulcanusMutation(s): 0 
Gene Names: psbV
Membrane Entity: Yes 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein XQ [auth X],
KA [auth x]
34Thermostichus vulcanusMutation(s): 0 
Gene Names: psbX
Membrane Entity: Yes 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein ycf12R [auth Y],
LA [auth y]
28Thermostichus vulcanusMutation(s): 0 
Gene Names: ycf12psbY
Membrane Entity: Yes 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein YS [auth N],
MA [auth n]
23Thermostichus vulcanusMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZT [auth Z],
NA [auth z]
62Thermostichus vulcanusMutation(s): 0 
Gene Names: psbZ
Membrane Entity: Yes 
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Small Molecules
Ligands 11 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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GC [auth C],
HC [auth C],
IC [auth C],
IE [auth b],
RB [auth B],
GC [auth C],
HC [auth C],
IC [auth C],
IE [auth b],
RB [auth B],
WE [auth c],
XE [auth c],
YE [auth c]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
 Ligand Interaction
CLA
Query on CLA

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AB [auth B],
AC [auth C],
AE [auth b],
BB [auth B],
BC [auth C],
AB [auth B],
AC [auth C],
AE [auth b],
BB [auth B],
BC [auth C],
BE [auth b],
CB [auth B],
CC [auth C],
CE [auth b],
CF [auth d],
DB [auth B],
DC [auth C],
DE [auth b],
DF [auth d],
EB [auth B],
FB [auth B],
GB [auth B],
HB [auth B],
HD [auth a],
IB [auth B],
ID [auth a],
JB [auth B],
JD [auth a],
JE [auth c],
KB [auth B],
KC [auth D],
KE [auth c],
KF [auth h],
LB [auth B],
LE [auth c],
ME [auth c],
MF [auth k],
NC [auth D],
NE [auth c],
OC [auth D],
OE [auth c],
PA [auth A],
PD [auth b],
PE [auth c],
QA [auth A],
QD [auth b],
QE [auth c],
RA [auth A],
RD [auth b],
RE [auth c],
SB [auth C],
SD [auth b],
SE [auth c],
TB [auth C],
TD [auth b],
TE [auth c],
UB [auth C],
UD [auth b],
UE [auth c],
VB [auth C],
VC [auth H],
VD [auth b],
WB [auth C],
WD [auth b],
XA [auth B],
XB [auth C],
XC [auth K],
XD [auth b],
YA [auth B],
YB [auth C],
YD [auth b],
ZA [auth B],
ZB [auth C],
ZD [auth b],
ZE [auth d]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
 Ligand Interaction
PHO
Query on PHO

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AF [auth d],
KD [auth a],
LC [auth D],
SA [auth A]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
 Ligand Interaction
LHG
Query on LHG

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ND [auth a],
VA [auth A]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
 Ligand Interaction
MGE
Query on MGE

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GF [auth d],
HE [auth b],
HF [auth d],
PF [auth l],
QB [auth B],
GF [auth d],
HE [auth b],
HF [auth d],
PF [auth l],
QB [auth B],
RC [auth D],
SC [auth D],
ZC [auth L]
(1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE
C38 H72 O10
FIJGNIAJTZSERN-DQQGJSMTSA-N
 Ligand Interaction
HEM
Query on HEM

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DD [auth V],
JF [auth f],
SF [auth v],
UC [auth F]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
PQ9
Query on PQ9

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EF [auth d],
LD [auth a],
PC [auth D],
TA [auth A]
5-[(2E,6E,10E,14E,18E,22E)-3,7,11,15,19,23,27-HEPTAMETHYLOCTACOSA-2,6,10,14,18,22,26-HEPTAENYL]-2,3-DIMETHYLBENZO-1,4-QUINONE
C43 H64 O2
JXUCGUASMMLSBH-HOHOQCMASA-N
 Ligand Interaction
BCR
Query on BCR

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BD [auth T],
CD [auth T],
EC [auth C],
ED [auth Z],
EE [auth b],
BD [auth T],
CD [auth T],
EC [auth C],
ED [auth Z],
EE [auth b],
FC [auth C],
FE [auth b],
FF [auth d],
LF [auth h],
MB [auth B],
MD [auth a],
NB [auth B],
NF [auth k],
OB [auth B],
OF [auth k],
QC [auth D],
QF [auth t],
TF [auth z],
UA [auth A],
VE [auth c],
WC [auth H],
YC [auth K]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
OEC
Query on OEC

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FD [auth a],
OA [auth A]
OXYGEN EVOLVING SYSTEM
Ca Mn4 O4
UFRGXNUNWYSFQE-MBOUAFFSAW
 Ligand Interaction
IOD
Query on IOD

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AD [auth T],
BF [auth d],
GE [auth b],
IF [auth d],
MC [auth D],
AD [auth T],
BF [auth d],
GE [auth b],
IF [auth d],
MC [auth D],
OD [auth a],
PB [auth B],
RF [auth t],
TC [auth D],
WA [auth A]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
FE2
Query on FE2

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GD [auth a],
JC [auth D]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 0.326 
  • R-Value Work: 0.290 
  • R-Value Observed: 0.290 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.499α = 90
b = 224.702β = 90
c = 304.919γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-05-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance