5TIS

Room temperature XFEL structure of the native, doubly-illuminated photosystem II complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Structure of photosystem II and substrate binding at room temperature.

Young, I.D.Ibrahim, M.Chatterjee, R.Gul, S.Fuller, F.D.Koroidov, S.Brewster, A.S.Tran, R.Alonso-Mori, R.Kroll, T.Michels-Clark, T.Laksmono, H.Sierra, R.G.Stan, C.A.Hussein, R.Zhang, M.Douthit, L.Kubin, M.de Lichtenberg, C.Vo Pham, L.Nilsson, H.Cheah, M.H.Shevela, D.Saracini, C.Bean, M.A.Seuffert, I.Sokaras, D.Weng, T.C.Pastor, E.Weninger, C.Fransson, T.Lassalle, L.Brauer, P.Aller, P.Docker, P.T.Andi, B.Orville, A.M.Glownia, J.M.Nelson, S.Sikorski, M.Zhu, D.Hunter, M.S.Lane, T.J.Aquila, A.Koglin, J.E.Robinson, J.Liang, M.Boutet, S.Lyubimov, A.Y.Uervirojnangkoorn, M.Moriarty, N.W.Liebschner, D.Afonine, P.V.Waterman, D.G.Evans, G.Wernet, P.Dobbek, H.Weis, W.I.Brunger, A.T.Zwart, P.H.Adams, P.D.Zouni, A.Messinger, J.Bergmann, U.Sauter, N.K.Kern, J.Yachandra, V.K.Yano, J.

(2016) Nature 540: 453-457

  • DOI: 10.1038/nature20161
  • Primary Citation of Related Structures:  
    5KAF, 5KAI, 5TIS

  • PubMed Abstract: 
  • Light-induced oxidation of water by photosystem II (PS II) in plants, algae and cyanobacteria has generated most of the dioxygen in the atmosphere. PS II, a membrane-bound multi-subunit pigment protein complex, couples the one-electron photochemistry at the reaction centre with the four-electron redox chemistry of water oxidation at the Mn 4 CaO 5 cluster in the oxygen-evolving complex (OEC) ...

    Light-induced oxidation of water by photosystem II (PS II) in plants, algae and cyanobacteria has generated most of the dioxygen in the atmosphere. PS II, a membrane-bound multi-subunit pigment protein complex, couples the one-electron photochemistry at the reaction centre with the four-electron redox chemistry of water oxidation at the Mn 4 CaO 5 cluster in the oxygen-evolving complex (OEC). Under illumination, the OEC cycles through five intermediate S-states (S 0 to S 4 ), in which S 1 is the dark-stable state and S 3 is the last semi-stable state before O-O bond formation and O 2 evolution. A detailed understanding of the O-O bond formation mechanism remains a challenge, and will require elucidation of both the structures of the OEC in the different S-states and the binding of the two substrate waters to the catalytic site. Here we report the use of femtosecond pulses from an X-ray free electron laser (XFEL) to obtain damage-free, room temperature structures of dark-adapted (S 1 ), two-flash illuminated (2F; S 3 -enriched), and ammonia-bound two-flash illuminated (2F-NH 3 ; S 3 -enriched) PS II. Although the recent 1.95 Å resolution structure of PS II at cryogenic temperature using an XFEL provided a damage-free view of the S 1 state, measurements at room temperature are required to study the structural landscape of proteins under functional conditions, and also for in situ advancement of the S-states. To investigate the water-binding site(s), ammonia, a water analogue, has been used as a marker, as it binds to the Mn 4 CaO 5 cluster in the S 2 and S 3 states. Since the ammonia-bound OEC is active, the ammonia-binding Mn site is not a substrate water site. This approach, together with a comparison of the native dark and 2F states, is used to discriminate between proposed O-O bond formation mechanisms.


    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

    Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II protein D1 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 CP47 reaction center 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 reaction center 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 Ycf12Q [auth Y], KA [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 ZS [auth Z], MA [auth z]62Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbZtsr1967
Membrane Entity: Yes 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II protein YT [auth R], NA [auth r]41Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbYtsl0836
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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JH [auth h], NG [auth c], OG [auth c], PG [auth c], SD [auth H], XC [auth C], YC [auth C], ZC [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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AB [auth A] , AG [auth c] , BF [auth b] , BG [auth c] , CF [auth b] , CG [auth c] , DF [auth b] , DG [auth c] , 
AB [auth A], AG [auth c], BF [auth b], BG [auth c], CF [auth b], CG [auth c], DF [auth b], DG [auth c], EF [auth b], EG [auth c], FD [auth D], FF [auth b], FG [auth c], GB [auth B], GD [auth D], GF [auth b], GG [auth c], HB [auth B], HF [auth b], HG [auth c], IB [auth B], IC [auth C], IF [auth b], IG [auth c], JB [auth B], JC [auth C], JF [auth b], JG [auth c], KB [auth B], KC [auth C], KF [auth b], KG [auth c], LB [auth B], LC [auth C], LF [auth b], MB [auth B], MC [auth C], MF [auth b], NB [auth B], NC [auth C], NE [auth a], NF [auth b], OB [auth B], OC [auth C], OE [auth a], OF [auth b], PB [auth B], PC [auth C], PF [auth b], QB [auth B], QC [auth C], QF [auth b], RB [auth B], RC [auth C], RE [auth a], SB [auth B], SC [auth C], TA [auth A], TB [auth B], TC [auth C], UA [auth A], UB [auth B], UC [auth C], VB [auth B], WA [auth A], WE [auth a], XG [auth d], YF [auth c], YG [auth d], 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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ED [auth D], PE [auth a], QE [auth a], VA [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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DB [auth A] , DC [auth B] , EC [auth B] , HH [auth f] , LD [auth D] , MD [auth D] , UE [auth a] , VF [auth b] , 
DB [auth A], DC [auth B], EC [auth B], HH [auth f], LD [auth D], MD [auth D], UE [auth a], VF [auth b], ZA [auth A], ZD [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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AC [auth B] , AD [auth C] , BD [auth C] , DH [auth d] , EH [auth d] , FC [auth B] , HC [auth C] , KD [auth D] , 
AC [auth B], AD [auth C], BD [auth C], DH [auth d], EH [auth d], FC [auth B], HC [auth C], KD [auth D], PH [auth m], QG [auth c], RG [auth c], UF [auth b], VE [auth a], ZB [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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AH [auth d], ID [auth D], TE [auth a], YA [auth A]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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AE [auth L] , BB [auth A] , BH [auth d] , CC [auth B] , CH [auth d] , FB [auth A] , JD [auth D] , NH [auth l] , 
AE [auth L], BB [auth A], BH [auth d], CC [auth B], CH [auth d], FB [auth A], JD [auth D], NH [auth l], XE [auth a], YE [auth a]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
 Ligand Interaction
HEC (Subject of Investigation/LOI)
Query on HEC

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GE [auth V], TH [auth v]HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
HEM (Subject of Investigation/LOI)
Query on HEM

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GH [auth e], PD [auth E]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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DE [auth T] , HD [auth D] , HE [auth Y] , IH [auth h] , LG [auth c] , MG [auth c] , RD [auth H] , RF [auth b] , 
DE [auth T], HD [auth D], HE [auth Y], IH [auth h], LG [auth c], MG [auth c], RD [auth H], RF [auth b], RH [auth t], SE [auth a], SF [auth b], SG [auth c], TF [auth b], TG [auth c], VC [auth C], WB [auth B], WC [auth C], XA [auth A], XB [auth B], YB [auth B], YD [auth K], ZG [auth d]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
OEX (Subject of Investigation/LOI)
Query on OEX

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

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ME [auth a], SA [auth A]BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
 Ligand Interaction
FE2
Query on FE2

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

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KE [auth a], LE [auth a], QA [auth A], RA [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
UNL
Query on UNL

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AF [auth a] , BC [auth B] , BE [auth M] , CB [auth A] , CD [auth C] , CE [auth M] , DD [auth C] , EB [auth A] , 
AF [auth a], BC [auth B], BE [auth M], CB [auth A], CD [auth C], CE [auth M], DD [auth C], EB [auth A], EE [auth T], FE [auth T], FH [auth d], GC [auth B], KH [auth i], LH [auth j], MH [auth j], ND [auth D], OD [auth D], OH [auth m], QD [auth E], QH [auth m], SH [auth t], TD [auth H], UD [auth I], UG [auth c], UH [auth x], VD [auth I], VG [auth c], WD [auth J], WF [auth b], WG [auth c], XD [auth J], XF [auth b], ZE [auth a]
Unknown ligand
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME
BA [auth i], H [auth I]L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.87α = 90
b = 223.14β = 90
c = 310.71γ = 90
Software Package:
Software NamePurpose
cctbx.xfeldata reduction
PHASERphasing
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Director, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences, Department of EnergyDepartment of EnergyUnited StatesDE-AC02-05CH11231
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 StatesGM110501
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
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5 F32 GM116423-02
Human Frontier Science Program (HFSP)FranceRGP0063/2013 310
German Research Foundation (DFG)Germany--
Deutsche forschungs GemeinschaftGermanySfb1078, TP A5
Umea University, Solar Fuels Strong Research EnvironmentSweden--
K&A Wallenberg FoundationSweden2011.0055
EnergimyndighetenSweden36648-1
Howard Hughes Medical Institute (HHMI)United StatesCollaborative Innovation Award
Collaborative Computational Project No. 4 (CCP4)United Kingdom--
National Energy Research Scientific Computing Center, Office of Science, Department of EnergyUnited StatesDE-AC02-05CH11231
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41GM103393
Linac Coherent Light Source (LCLS) and SSRL, SLAC National Accelerator Laboratory, Office of Basic Energy Science, Department of EnergyUnited StatesDE-AC02-76SF00515
Brookhaven National Laboratory, Department of EnergyUnited StatesLaboratory Directed Research and Development grant 11-008
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United States2-P41-RR012408
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States8P41GM103473-16
Department of Energy (DOE, United States)United StatesFWP BO-70
Biotechnology and Biological Sciences Research Council (BBSRC)United Kingdom102593
Department of Energy (DOE, United States)United StatesDE-AC02-98CH10886
Department of Energy (DOE, United States)United StatesDE-SC0012704
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41GM111244

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-23
    Type: Initial release
  • Version 1.1: 2016-12-14
    Changes: Database references
  • Version 1.2: 2016-12-28
    Changes: Database references
  • Version 1.3: 2017-09-27
    Changes: Author supporting evidence, Data collection, Refinement description
  • Version 1.4: 2019-11-20
    Changes: Author supporting evidence
  • Version 1.5: 2020-01-01
    Changes: Author supporting evidence
  • Version 2.0: 2021-03-10
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary