3KZI

Crystal Structure of Monomeric Form of Cyanobacterial Photosystem II


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.297 
  • R-Value Observed: 0.297 

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Literature

Crystal Structure of Monomeric Photosystem II from Thermosynechococcus elongatus at 3.6-A Resolution

Broser, M.Gabdulkhakov, A.Kern, J.Guskov, A.Muh, F.Saenger, W.Zouni, A.

(2010) J Biol Chem 285: 26255-26262

  • DOI: 10.1074/jbc.M110.127589
  • Primary Citation of Related Structures:  
    3KZI

  • PubMed Abstract: 
  • The membrane-embedded photosystem II core complex (PSIIcc) uses light energy to oxidize water in photosynthesis. Information about the spatial structure of PSIIcc obtained from x-ray crystallography was so far derived from homodimeric PSIIcc of thermophilic cyanobacteria ...

    The membrane-embedded photosystem II core complex (PSIIcc) uses light energy to oxidize water in photosynthesis. Information about the spatial structure of PSIIcc obtained from x-ray crystallography was so far derived from homodimeric PSIIcc of thermophilic cyanobacteria. Here, we report the first crystallization and structural analysis of the monomeric form of PSIIcc with high oxygen evolution capacity, isolated from Thermosynechococcus elongatus. The crystals belong to the space group C222(1), contain one monomer per asymmetric unit, and diffract to a resolution of 3.6 A. The x-ray diffraction pattern of the PSIIcc-monomer crystals exhibit less anisotropy (dependence of resolution on crystal orientation) compared with crystals of dimeric PSIIcc, and the packing of the molecules within the unit cell is different. In the monomer, 19 protein subunits, 35 chlorophylls, two pheophytins, the non-heme iron, the primary plastoquinone Q(A), two heme groups, 11 beta-carotenes, 22 lipids, seven detergent molecules, and the Mn(4)Ca cluster of the water oxidizing complex could be assigned analogous to the dimer. Based on the new structural information, the roles of lipids and protein subunits in dimer formation of PSIIcc are discussed. Due to the lack of non-crystallographic symmetry and the orientation of the membrane normal of PSIIcc perpendicular ( approximately 87 degrees ) to the crystallographic b-axis, further information about the structure of the Mn(4)Ca cluster is expected to become available from orientation-dependent spectroscopy on this new crystal form.


    Organizational Affiliation

    Institute of Chemistry, Max Volmer Laboratory of Biophysical Chemistry, Technische Universität Berlin, Berlin, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem Q(B) protein 1A344Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbA1psbA-1tlr1843
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II core light harvesting proteinB510Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbBtlr1530
Membrane Entity: Yes 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II CP43 proteinC461Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbCtlr1631
Membrane Entity: Yes 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II D2 proteinD352Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbD1tlr0455psbD2tlr1630
EC: 1.10.3.9
Membrane Entity: Yes 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaE83Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbEtsr1541
Membrane Entity: Yes 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaF44Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbFtsr1542
Membrane Entity: Yes 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein HG [auth H]65Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbHtsl1386
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein IH [auth I]38Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbItsr1074
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein JI [auth J]40Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbJtsr1544
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein KJ [auth K]37Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbKtsl0176
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein LK [auth L]37Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbLtsr1543
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein ML [auth M]36Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbMtsl2052
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II manganese-stabilizing polypeptideM [auth O]246Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbOtll0444
Membrane Entity: Yes 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein TN [auth T]32Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbTtsr1531
Membrane Entity: Yes 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II 12 kDa extrinsic proteinO [auth U]104Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbUtll2409
Membrane Entity: Yes 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c-550P [auth V]137Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbVtll1285
Membrane Entity: Yes 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein ycf12Q [auth y]46Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: ycf12tsr1242
Membrane Entity: Yes 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center X proteinR [auth X]40Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbXtsr2013
Membrane Entity: Yes 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZS [auth Z]62Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbZtsr1967
Membrane Entity: Yes 
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  • Reference Sequence
Small Molecules
Ligands 15 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DGD (Subject of Investigation/LOI)
Query on DGD

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AB [auth B], CB [auth B], DA [auth A], DB [auth C], IC [auth D], UB [auth C], VB [auth C], WB [auth C]DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
 Ligand Interaction
CLA (Subject of Investigation/LOI)
Query on CLA

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AC [auth D] , CC [auth D] , FA [auth A] , GA [auth B] , GB [auth C] , HA [auth B] , HB [auth C] , IA [auth B] , 
AC [auth D], CC [auth D], FA [auth A], GA [auth B], GB [auth C], HA [auth B], HB [auth C], IA [auth B], IB [auth C], JA [auth B], JB [auth C], KA [auth B], KB [auth C], LA [auth B], LB [auth C], MA [auth B], MB [auth C], NA [auth B], NB [auth C], OA [auth B], OB [auth C], PA [auth B], PB [auth C], QA [auth B], QB [auth C], RA [auth B], RB [auth C], SA [auth B], SC [auth K], TA [auth B], U [auth A], UA [auth B], V [auth A], VA [auth B], X [auth A]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
 Ligand Interaction
PHO (Subject of Investigation/LOI)
Query on PHO

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BC [auth D], W [auth A]PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
 Ligand Interaction
SQD (Subject of Investigation/LOI)
Query on SQD

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EB [auth C], HC [auth D], LC [auth F], UC [auth L]1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
 Ligand Interaction
LMG (Subject of Investigation/LOI)
Query on LMG

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CA [auth A], FC [auth D], GC [auth D], NC [auth I], PC [auth J], VC [auth M], XB [auth C], ZA [auth B]1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
 Ligand Interaction
PL9 (Subject of Investigation/LOI)
Query on PL9

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DC [auth D]2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE
C53 H80 O2
FKUYMLZIRPABFK-UHFFFAOYSA-N
 Ligand Interaction
LHG (Subject of Investigation/LOI)
Query on LHG

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BA [auth A], FB [auth C]1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
 Ligand Interaction
HEM (Subject of Investigation/LOI)
Query on HEM

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KC [auth F], ZC [auth V]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
BCR (Subject of Investigation/LOI)
Query on BCR

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AA [auth A] , AD [auth X] , BD [auth Z] , EC [auth D] , QC [auth J] , RC [auth J] , SB [auth C] , TB [auth C] , 
AA [auth A], AD [auth X], BD [auth Z], EC [auth D], QC [auth J], RC [auth J], SB [auth C], TB [auth C], WA [auth B], XA [auth B], YA [auth B]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
LMT (Subject of Investigation/LOI)
Query on LMT

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BB [auth B], EA [auth A], JC [auth D], OC [auth I], XC [auth O], YB [auth D], YC [auth T]DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
OEC (Subject of Investigation/LOI)
Query on OEC

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Z [auth A]OXYGEN EVOLVING SYSTEM
Ca Mn4 O4
UFRGXNUNWYSFQE-MBOUAFFSAW
 Ligand Interaction
MES
Query on MES

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Y [auth A]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
BCT
Query on BCT

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ZB [auth D]BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
 Ligand Interaction
FE2
Query on FE2

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T [auth A]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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MC [auth F], TC [auth K], WC [auth O]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.297 
  • R-Value Observed: 0.297 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.89α = 90
b = 224.69β = 90
c = 337.28γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
CNSrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-06-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance