4TNI

RT XFEL structure of Photosystem II 500 ms after the third illumination at 4.6 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.60 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.278 
  • R-Value Observed: 0.278 

wwPDB Validation   3D Report Full Report


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 flashe ...

    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 1Aa344Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbA1psbA-1tlr1843
EC: 1.10.3.9
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II core light harvesting proteinBb510Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbBtlr1530
Find proteins for Q8DIQ1 (Thermosynechococcus elongatus (strain BP-1))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II CP43 proteinCc461Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbCtlr1631
Find proteins for Q8DIF8 (Thermosynechococcus elongatus (strain BP-1))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II D2 proteinDd352Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbD1tlr0455psbD2tlr1630
EC: 1.10.3.9
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaEe84Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbEtsr1541
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaFf45Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbFtsr1542
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein HHh66Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbHtsl1386
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein IIi38Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbItsr1074
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Entity ID: 9
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Photosystem II reaction center protein JJj40Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbJtsr1544
Find proteins for P59087 (Thermosynechococcus elongatus (strain BP-1))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein KKk46Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbKtsl0176
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein LLl37Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbLtsr1543
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein MMm36Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbMtsl2052
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II manganese-stabilizing polypeptideOo272Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbOtll0444
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein TTt32Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbTtsr1531
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II 12 kDa extrinsic proteinUu134Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbUtll2409
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c-550Vv163Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbVtll1285
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12gy46Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: ycf12tsr1242
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center X proteinXx41Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbXtsr2013
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Entity ID: 19
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Photosystem II reaction center protein YGY28Thermosynechococcus elongatus BP-1Mutation(s): 0 
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Entity ID: 20
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Photosystem II reaction center protein ZZz62Thermosynechococcus elongatus BP-1Mutation(s): 0 
Gene Names: psbZtsr1967
Find proteins for Q8DHJ2 (Thermosynechococcus elongatus (strain BP-1))
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  • Reference Sequence
Small Molecules
Ligands 15 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

Download Ideal Coordinates CCD File 
A, B, C, D, a, b, c, d
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
 Ligand Interaction
CLA
Query on CLA

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A, B, C, D, H, a, b, c, d, h
CHLOROPHYLL A
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-AENOIHSZSA-M
 Ligand Interaction
PHO
Query on PHO

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D, d
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
 Ligand Interaction
SQD
Query on SQD

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A, B, F, a, b, d, f
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
Query on LMG

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A, B, C, D, E, I, M, a, b, c, d, e, i, m
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
 Ligand Interaction
PL9
Query on PL9

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A, D, J, a, d, j
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
Query on LHG

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A, C, a, c
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
 Ligand Interaction
HEM
Query on HEM

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F, V, f, v
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
BCR
Query on BCR

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A, B, C, F, H, J, K, a, b, c, f, g, j, x, y
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
LMT
Query on LMT

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B, D, I, M, b, d, i
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
OEX
Query on OEX

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A, a
CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
 Ligand Interaction
BCT
Query on BCT

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D, d
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
 Ligand Interaction
FE2
Query on FE2

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

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K, O, k, o
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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D, a
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.60 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.278 
  • R-Value Observed: 0.278 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.433α = 90
b = 228.809β = 90
c = 307.918γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
cctbx.xfeldata reduction

Structure Validation

View Full Validation Report



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

Revision History 

  • 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