4TNH

RT XFEL structure of Photosystem II in the dark state at 4.9 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.90 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.281 
  • R-Value Observed: 0.281 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy.

Kern, J.Tran, R.Alonso-Mori, R.Koroidov, S.Echols, N.Hattne, J.Ibrahim, M.Gul, S.Laksmono, H.Sierra, R.G.Gildea, R.J.Han, G.Hellmich, J.Lassalle-Kaiser, B.Chatterjee, R.Brewster, A.S.Stan, C.A.Glockner, C.Lampe, A.DiFiore, D.Milathianaki, D.Fry, A.R.Seibert, M.M.Koglin, J.E.Gallo, E.Uhlig, J.Sokaras, D.Weng, T.C.Zwart, P.H.Skinner, D.E.Bogan, M.J.Messerschmidt, M.Glatzel, P.Williams, G.J.Boutet, S.Adams, P.D.Zouni, A.Messinger, J.Sauter, N.K.Bergmann, U.Yano, J.Yachandra, V.K.

(2014) Nat Commun 5: 4371-4371

  • DOI: 10.1038/ncomms5371
  • Primary Citation of Related Structures:  
    4TNH, 4TNI, 4TNJ, 4TNK, 4TNL

  • PubMed Abstract: 
  • The dioxygen we breathe is formed by light-induced oxidation of water in photosystem II. O2 formation takes place at a catalytic manganese cluster within milliseconds after the photosystem II reaction centre is excited by three single-turnover flashes. Here we present combined X-ray emission spectra and diffraction data of 2-flash (2F) and 3-flash (3F) photosystem II samples, and of a transient 3F' state (250 μs after the third flash), collected under functional conditions using an X-ray free electron laser ...

    The dioxygen we breathe is formed by light-induced oxidation of water in photosystem II. O2 formation takes place at a catalytic manganese cluster within milliseconds after the photosystem II reaction centre is excited by three single-turnover flashes. Here we present combined X-ray emission spectra and diffraction data of 2-flash (2F) and 3-flash (3F) photosystem II samples, and of a transient 3F' state (250 μs after the third flash), collected under functional conditions using an X-ray free electron laser. The spectra show that the initial O-O bond formation, coupled to Mn reduction, does not yet occur within 250 μs after the third flash. Diffraction data of all states studied exhibit an anomalous scattering signal from Mn but show no significant structural changes at the present resolution of 4.5 Å. This study represents the initial frames in a molecular movie of the structural changes during the catalytic reaction in photosystem II.


    Related Citations: 
    • Towards automated crystallographic structure refinement with phenix.refine.
      Afonine, P.V., Grosse-Kunstleve, R.W., Echols, N., Headd, J.J., Moriarty, N.W., Mustyakimov, M., Terwilliger, T.C., Urzhumtsev, A., Zwart, P.H., Adams, P.D.
      (2012) Acta Crystallogr D Biol Crystallogr 68: 352
    • PHENIX: a comprehensive Python-based system for macromolecular structure solution.
      Adams, P.D., Afonine, P.V., Bunkoczi, G., Chen, V.B., Davis, I.W., Echols, N., Headd, J.J., Hung, L.W., Kapral, G.J., Grosse-Kunstleve, R.W., McCoy, A.J., Moriarty, N.W., Oeffner, R., Read, R.J., Richardson, D.C., Richardson, J.S., Terwilliger, T.C., Zwart, P.H.
      (2010) Acta Crystallogr D Biol Crystallogr 66: 213

    Organizational Affiliation

    Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem Q(B) protein 1A, U [auth a]344Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbA1psbA-1tlr1843
EC: 1.10.3.9
Membrane Entity: Yes 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II core light harvesting proteinB, V [auth b]510Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbBtlr1530
Membrane Entity: Yes 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II CP43 proteinC, W [auth c]461Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbCtlr1631
Membrane Entity: Yes 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II D2 proteinD, X [auth d]352Thermosynechococcus 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 alphaE, Y [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, Z [auth f]45Thermosynechococcus 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], AA [auth h]66Thermosynechococcus 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], BA [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], CA [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], DA [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], EA [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], FA [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], GA [auth o]272Thermosynechococcus 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], HA [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], IA [auth u]134Thermosynechococcus 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], JA [auth v]163Thermosynechococcus 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 Ycf12KA [auth g], Q [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], LA [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 YMA [auth G], S [auth Y]28Thermosynechococcus vestitus BP-1Mutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZT [auth Z], NA [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

Download Ideal Coordinates CCD File 
BC [auth B] , HG [auth c] , ID [auth D] , IG [auth c] , JG [auth c] , NE [auth a] , PF [auth b] , SE [auth b] , 
BC [auth B], HG [auth c], ID [auth D], IG [auth c], JG [auth c], NE [auth a], PF [auth b], SE [auth b], TC [auth C], UC [auth C], VA [auth A], VC [auth C], WB [auth B], XG [auth d]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
 Ligand Interaction
CLA (Subject of Investigation/LOI)
Query on CLA

Download Ideal Coordinates CCD File 
AF [auth b] , AG [auth c] , BF [auth b] , BG [auth c] , CF [auth b] , CG [auth c] , DB [auth B] , DD [auth D] , 
AF [auth b], AG [auth c], BF [auth b], BG [auth c], CF [auth b], CG [auth c], DB [auth B], DD [auth D], DF [auth b], DG [auth c], EB [auth B], ED [auth D], EF [auth b], EG [auth c], EH [auth h], FB [auth B], FC [auth C], FF [auth b], GB [auth B], GC [auth C], GE [auth a], GF [auth b], HB [auth B], HC [auth C], HE [auth a], HF [auth b], IB [auth B], IC [auth C], IE [auth a], IF [auth b], JB [auth B], JC [auth C], JF [auth b], KB [auth B], KC [auth C], KE [auth a], KF [auth b], LB [auth B], LC [auth C], MB [auth B], MC [auth C], MG [auth c], NB [auth B], NC [auth C], OB [auth B], OC [auth C], PA [auth A], PB [auth B], PC [auth C], PD [auth H], QA [auth A], QB [auth B], QC [auth C], RA [auth A], RB [auth B], SA [auth A], SG [auth d], TF [auth c], TG [auth d], UF [auth c], VF [auth c], WE [auth b], WF [auth c], XE [auth b], XF [auth c], YC [auth C], YE [auth b], YF [auth c], 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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AD [auth D], BD [auth D], JE [auth a], PG [auth d]PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
 Ligand Interaction
SQD (Subject of Investigation/LOI)
Query on SQD

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AB [auth A] , BB [auth A] , CC [auth B] , DE [auth a] , DH [auth f] , OD [auth F] , QG [auth d] , RE [auth a] , 
AB [auth A], BB [auth A], CC [auth B], DE [auth a], DH [auth f], OD [auth F], QG [auth d], RE [auth a], TE [auth b], YB [auth B]
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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AH [auth e] , CB [auth A] , EE [auth a] , FH [auth i] , GD [auth D] , HD [auth D] , KD [auth D] , KG [auth c] , 
AH [auth e], CB [auth A], EE [auth a], FH [auth i], GD [auth D], HD [auth D], KD [auth D], KG [auth c], KH [auth l], LD [auth E], LH [auth m], OG [auth c], QF [auth b], RD [auth I], VG [auth d], WC [auth C], WG [auth d], XA [auth A], XB [auth B], XD [auth M], ZC [auth C], ZG [auth d]
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], HH [auth j], LE [auth a], TA [auth A], TD [auth J], UG [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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LG [auth c], OE [auth a], WA [auth A], XC [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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BE [auth V], BH [auth f], MD [auth F], NH [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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CE [auth y] , CH [auth f] , FG [auth c] , GG [auth c] , IH [auth j] , LF [auth b] , ME [auth a] , MF [auth b] , 
CE [auth y], CH [auth f], FG [auth c], GG [auth c], IH [auth j], LF [auth b], ME [auth a], MF [auth b], ND [auth F], NF [auth b], NG [auth c], OF [auth b], OH [auth g], PH [auth x], QD [auth H], RC [auth C], SB [auth B], SC [auth C], TB [auth B], UA [auth A], UB [auth B], UD [auth J], VB [auth B], WD [auth K]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
LMT (Subject of Investigation/LOI)
Query on LMT

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AC [auth B] , DC [auth B] , EC [auth B] , GH [auth i] , JD [auth D] , RF [auth b] , SD [auth I] , SF [auth b] , 
AC [auth B], DC [auth B], EC [auth B], GH [auth i], JD [auth D], RF [auth b], SD [auth I], SF [auth b], UE [auth b], VE [auth b], YD [auth M], YG [auth d], ZB [auth B], ZD [auth M]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
OEX (Subject of Investigation/LOI)
Query on OEX

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QE [auth a], ZA [auth A]CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
 Ligand Interaction
BCT
Query on BCT

Download Ideal Coordinates CCD File 
CD [auth D], RG [auth d]BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
 Ligand Interaction
FE2
Query on FE2

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

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AE [auth O], JH [auth k], MH [auth o], VD [auth K]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
PE [auth a], YA [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.90 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.281 
  • R-Value Observed: 0.281 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.885α = 90
b = 229.033β = 90
c = 307.715γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
cctbx.xfeldata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM055302
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41GM103393
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM095887
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM102520
Department of Energy (DOE, United States)United StatesDE-AC02-05CH11231

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-07-23
    Changes: Database references
  • Version 1.2: 2015-10-07
    Changes: Other
  • Version 1.3: 2017-09-27
    Changes: Author supporting evidence, Derived calculations, Refinement description
  • Version 1.4: 2019-12-04
    Changes: Author supporting evidence