5MX2

Photosystem II depleted of the Mn4CaO5 cluster at 2.55 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Structural insights into the light-driven auto-assembly process of the water-oxidizing Mn4CaO5-cluster in photosystem II.

Zhang, M.Bommer, M.Chatterjee, R.Hussein, R.Yano, J.Dau, H.Kern, J.Dobbek, H.Zouni, A.

(2017) Elife 6

  • DOI: 10.7554/eLife.26933
  • Primary Citation of Related Structures:  
    5MX2

  • PubMed Abstract: 
  • In plants, algae and cyanobacteria, Photosystem II (PSII) catalyzes the light-driven splitting of water at a protein-bound Mn 4 CaO 5 -cluster, the water-oxidizing complex (WOC). In the photosynthetic organisms, the light-driven formation of the WOC from dissolved metal ions is a key process because it is essential in both initial activation and continuous repair of PSII ...

    In plants, algae and cyanobacteria, Photosystem II (PSII) catalyzes the light-driven splitting of water at a protein-bound Mn 4 CaO 5 -cluster, the water-oxidizing complex (WOC). In the photosynthetic organisms, the light-driven formation of the WOC from dissolved metal ions is a key process because it is essential in both initial activation and continuous repair of PSII. Structural information is required for understanding of this chaperone-free metal-cluster assembly. For the first time, we obtained a structure of PSII from Thermosynechococcus elongatus without the Mn 4 CaO 5 -cluster. Surprisingly, cluster-removal leaves the positions of all coordinating amino acid residues and most nearby water molecules largely unaffected, resulting in a pre-organized ligand shell for kinetically competent and error-free photo-assembly of the Mn 4 CaO 5 -cluster. First experiments initiating (i) partial disassembly and (ii) partial re-assembly after complete depletion of the Mn 4 CaO 5 -cluster agree with a specific bi-manganese cluster, likely a di-µ-oxo bridged pair of Mn(III) ions, as an assembly intermediate.


    Organizational Affiliation

    Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II protein D1 1A, T [auth a]344Thermosynechococcus 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 CP47 reaction center proteinB, U [auth b]510Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbBtlr1530
Membrane Entity: Yes 
UniProt
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinC, V [auth c]461Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbCtlr1631
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II D2 proteinD, W [auth d]352Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbD1tlr0455psbD2tlr1630
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaE, X [auth e]84Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbEtsr1541
Membrane Entity: Yes 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaF, Y [auth f]45Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbFtsr1542
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein HG [auth H], Z [auth h]66Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbHtsl1386
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein IH [auth I], AA [auth i]38Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbItsr1074
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein JI [auth J], BA [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], CA [auth k]46Thermosynechococcus 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], DA [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], EA [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], FA [auth o]272Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbOtll0444
Membrane Entity: Yes 
UniProt
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein TN [auth T], GA [auth t]32Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbTtsr1531
Membrane Entity: Yes 
UniProt
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II 12 kDa extrinsic proteinO [auth U], HA [auth u]134Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbUtll2409
Membrane Entity: Yes 
UniProt
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c-550P [auth V], IA [auth v]163Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbVtll1285
Membrane Entity: Yes 
UniProt
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12Q [auth Y], MA [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], JA [auth x]41Thermosynechococcus 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], NA [auth z]62Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbZtsr1967
Membrane Entity: Yes 
UniProt
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II protein YKA [auth R], LA [auth r]41Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbYtsl0836
Membrane Entity: Yes 
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  • Reference Sequence
Small Molecules
Ligands 13 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DGD (Subject of Investigation/LOI)
Query on DGD

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JH [auth h], LG [auth c], MG [auth c], NG [auth c], SD [auth H], VC [auth C], WC [auth C], XC [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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AF [auth b] , AG [auth c] , BF [auth b] , BG [auth c] , CD [auth D] , CF [auth b] , CG [auth c] , DB [auth B] , 
AF [auth b], AG [auth c], BF [auth b], BG [auth c], CD [auth D], CF [auth b], CG [auth c], DB [auth B], DD [auth D], DF [auth b], DG [auth c], EB [auth B], EF [auth b], EG [auth c], FB [auth B], FF [auth b], FG [auth c], GB [auth B], GC [auth C], GF [auth b], GG [auth c], HB [auth B], HC [auth C], HE [auth a], HF [auth b], HG [auth c], IB [auth B], IC [auth C], IE [auth a], IF [auth b], IG [auth c], JB [auth B], JC [auth C], JF [auth b], JG [auth c], KB [auth B], KC [auth C], KE [auth a], LB [auth B], LC [auth C], MB [auth B], MC [auth C], NB [auth B], NC [auth C], OB [auth B], OC [auth C], PB [auth B], PC [auth C], QA [auth A], QB [auth B], QC [auth C], QD [auth H], RA [auth A], RB [auth B], RC [auth C], SC [auth C], TA [auth A], UE [auth b], UG [auth d], VE [auth b], VG [auth d], WE [auth b], WG [auth d], XE [auth b], XF [auth c], YE [auth b], YF [auth c], ZA [auth A], ZE [auth b], ZF [auth c]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
 Ligand Interaction
PHO (Subject of Investigation/LOI)
Query on PHO

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BD [auth D], JE [auth a], RE [auth a], SA [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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HH [auth f], LD [auth D], NE [auth a], PE [auth a], SE [auth b], WA [auth A], XD [auth L], YA [auth A]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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AD [auth C] , FC [auth C] , GH [auth f] , JD [auth D] , OG [auth c] , PF [auth b] , RG [auth c] , RH [auth m] , 
AD [auth C], FC [auth C], GH [auth f], JD [auth D], OG [auth c], PF [auth b], RG [auth c], RH [auth m], VB [auth B], WF [auth c], XB [auth B], YC [auth C]
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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FD [auth D], ME [auth a], VA [auth A], YG [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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AH [auth d] , EH [auth e] , GD [auth D] , HD [auth D] , ID [auth D] , OD [auth E] , OH [auth l] , TF [auth b] , 
AH [auth d], EH [auth e], GD [auth D], HD [auth D], ID [auth D], OD [auth E], OH [auth l], TF [auth b], YD [auth L], ZG [auth d]
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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DE [auth V], FH [auth e], PD [auth E], UH [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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BE [auth T] , ED [auth D] , IH [auth h] , KF [auth b] , KG [auth c] , LE [auth a] , LF [auth b] , MF [auth b] , 
BE [auth T], ED [auth D], IH [auth h], KF [auth b], KG [auth c], LE [auth a], LF [auth b], MF [auth b], NH [auth k], RD [auth H], SB [auth B], SG [auth c], TB [auth B], TC [auth C], TG [auth c], TH [auth t], UA [auth A], UB [auth B], UC [auth C], VD [auth K], WD [auth K], XG [auth d]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
LFA (Subject of Investigation/LOI)
Query on LFA

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AB [auth A] , AC [auth B] , AE [auth M] , BC [auth B] , BH [auth d] , CC [auth B] , CE [auth T] , CH [auth d] , 
AB [auth A], AC [auth B], AE [auth M], BC [auth B], BH [auth d], CC [auth B], CE [auth T], CH [auth d], DC [auth B], DH [auth d], EC [auth B], KD [auth D], KH [auth i], LH [auth i], MD [auth D], MH [auth j], ND [auth D], NF [auth b], OE [auth a], OF [auth b], PG [auth c], PH [auth m], QF [auth b], QG [auth c], QH [auth m], RF [auth b], SF [auth b], SH [auth t], TD [auth I], TE [auth b], UD [auth J], UF [auth b], VF [auth b], WB [auth B], XA [auth A], YB [auth B], ZB [auth B], ZC [auth C], ZD [auth M]
EICOSANE
C20 H42
CBFCDTFDPHXCNY-UHFFFAOYSA-N
 Ligand Interaction
BCT
Query on BCT

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CB [auth A], QE [auth a]BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
 Ligand Interaction
FE
Query on FE

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BB [auth A], EE [auth a]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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FE [auth a], GE [auth a], OA [auth A], PA [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.326α = 90
b = 219.617β = 90
c = 304.043γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB1078

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-02
    Type: Initial release
  • Version 1.1: 2018-02-21
    Changes: Database references
  • Version 1.2: 2018-03-28
    Changes: Data collection, Database references
  • Version 1.3: 2019-09-25
    Changes: Data collection, Derived calculations
  • Version 1.4: 2019-11-20
    Changes: Derived calculations