5H2F

Crystal structure of the PsbM-deletion mutant of photosystem II


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.177 

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Mutual relationships between structural and functional changes in a PsbM-deletion mutant of photosystem II.

Uto, S.Kawakami, K.Umena, Y.Iwai, M.Ikeuchi, M.Shen, J.R.Kamiya, N.

(2017) Faraday Discuss 198: 107-120

  • DOI: 10.1039/c6fd00213g
  • Primary Citation of Related Structures:  
    5H2F

  • PubMed Abstract: 
  • Photosystem II (PSII) is a membrane protein complex that performs light-induced electron transfer and oxygen evolution from water. PSII consists of 19 or 20 subunits in its crystal form and binds various cofactors such as chlorophyll a, plastoquinone, carotenoid, and lipids ...

    Photosystem II (PSII) is a membrane protein complex that performs light-induced electron transfer and oxygen evolution from water. PSII consists of 19 or 20 subunits in its crystal form and binds various cofactors such as chlorophyll a, plastoquinone, carotenoid, and lipids. After initial light excitation, the charge separation produces an electron, which is transferred to a plastoquinone molecule (Q A ) and then to another plastoquinone (Q B ). PsbM is a low-molecular-weight subunit with one transmembrane helix, and is located in the monomer-monomer interface of the PSII dimer. The function of PsbM has been reported to be stabilization of the PSII dimer and maintenance of electron transfer efficiency of PSII based on previous X-ray crystal structure analysis at a resolution of 4.2 Å. In order to elucidate the structure-function relationships of PsbM in detail, we improved the quality of PSII crystals from a PsbM-deleted mutant (ΔPsbM-PSII) of Thermosynechococcus elongatus, and succeeded in improving the diffraction quality to a resolution of 2.2 Å. X-ray crystal structure analysis of ΔPsbM-PSII showed that electron densities for the PsbM subunit and neighboring carotenoid and detergent molecules were absent in the monomer-monomer interface. The overall structure of ΔPsbM-PSII was similar to wild-type PSII, but the arrangement of the hydrophobic transmembrane subunits was significantly changed by the deletion of PsbM, resulting in a slight widening of the lipid hole involving Q B . The lipid hole-widening further induced structural changes of the bicarbonate ion coordinated to the non-heme Fe(ii) atom and destabilized the polypeptide chains around the Q B binding site located far from the position of PsbM. The fluorescence decay measurement indicated that the electron transfer rate from Q A to Q B was decreased in ΔPsbM-PSII compared with wild-type PSII. The functional change in electron transfer efficiency was fully interpreted based on structural changes caused by the deletion of the PsbM subunit.


    Organizational Affiliation

    Department of Chemistry, Graduate School of Science, Osaka City University, Osaka, Japan. nkamiya@sci.osaka-cu.ac.jp.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II protein D1 1A, S [auth a]334Thermosynechococcus 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, T [auth b]505Thermosynechococcus 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, U [auth c]455Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbCtlr1631
Membrane Entity: Yes 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II D2 proteinD, V [auth d]342Thermosynechococcus 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, W [auth e]80Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbEtsr1541
Membrane Entity: Yes 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaF, X [auth f]33Thermosynechococcus 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], Y [auth h]63Thermosynechococcus 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], Z [auth i]36Thermosynechococcus 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], AA [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], BA [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], CA [auth l]35Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbLtsr1543
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II manganese-stabilizing polypeptideL [auth O], DA [auth o]243Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbOtll0444
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein TM [auth T], EA [auth t]30Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbTtsr1531
Membrane Entity: Yes 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II 12 kDa extrinsic proteinN [auth U], FA [auth u]97Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbUtll2409
Membrane Entity: Yes 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c-550O [auth V], GA [auth v]137Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbVtll1285
Membrane Entity: Yes 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12P [auth Y], HA [auth y]29Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: ycf12tsr1242
Membrane Entity: Yes 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center X proteinQ [auth X], IA [auth x]37Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbXtsr2013
Membrane Entity: Yes 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZR [auth Z], JA [auth z]62Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: psbZtsr1967
Membrane Entity: Yes 
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Small Molecules
Ligands 21 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DGD (Subject of Investigation/LOI)
Query on DGD

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AM [auth h] , EK [auth c] , FF [auth H] , FK [auth c] , GK [auth c] , LD [auth C] , LL [auth d] , MD [auth C] , 
AM [auth h], EK [auth c], FF [auth H], FK [auth c], GK [auth c], LD [auth C], LL [auth d], MD [auth C], ND [auth C], PE [auth D]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
 Ligand Interaction
CLA (Subject of Investigation/LOI)
Query on CLA

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AD [auth C] , AK [auth c] , BD [auth C] , BK [auth c] , CD [auth C] , DD [auth C] , DI [auth b] , ED [auth C] , 
AD [auth C], AK [auth c], BD [auth C], BK [auth c], CD [auth C], DD [auth C], DI [auth b], ED [auth C], EI [auth b], FD [auth C], FI [auth b], GB [auth B], GD [auth C], GI [auth b], HB [auth B], HD [auth C], HI [auth b], HL [auth d], IB [auth B], ID [auth C], II [auth b], IL [auth d], JB [auth B], JE [auth D], JH [auth a], JI [auth b], KB [auth B], KH [auth a], KI [auth b], LB [auth B], LE [auth D], LH [auth a], LI [auth b], MB [auth B], ME [auth D], MI [auth b], NB [auth B], NI [auth b], OA [auth A], OB [auth B], OH [auth a], OI [auth b], PA [auth A], PB [auth B], PI [auth b], PJ [auth c], QB [auth B], QI [auth b], QJ [auth c], RA [auth A], RB [auth B], RI [auth b], RJ [auth c], SB [auth B], SI [auth b], SJ [auth c], TB [auth B], TJ [auth c], UB [auth B], UJ [auth c], VB [auth B], VJ [auth c], WC [auth C], WJ [auth c], XC [auth C], XJ [auth c], YC [auth C], YJ [auth c], ZC [auth C], ZJ [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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KE [auth D], MH [auth a], NH [auth a], QA [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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MM [auth l], QE [auth D], QH [auth a], UH [auth a], VC [auth C], WA [auth A], WI [auth b], WL [auth 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 (Subject of Investigation/LOI)
Query on LMG

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BM [auth i] , HK [auth c] , HM [auth j] , NF [auth J] , OD [auth C] , OL [auth d] , RK [auth c] , TA [auth A] , 
BM [auth i], HK [auth c], HM [auth j], NF [auth J], OD [auth C], OL [auth d], RK [auth c], TA [auth A], UE [auth D], XI [auth b], ZB [auth B], ZD [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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KL [auth d], OE [auth D], RH [auth a], UA [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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GL [auth d] , ML [auth d] , NL [auth d] , NM [auth l] , QD [auth C] , RE [auth D] , SE [auth D] , SF [auth L] , 
GL [auth d], ML [auth d], NL [auth d], NM [auth l], QD [auth C], RE [auth D], SE [auth D], SF [auth L], SH [auth a], TE [auth D], VA [auth A], ZH [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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LN [auth v], OG [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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CF [auth E], VL [auth e]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
RRX (Subject of Investigation/LOI)
Query on RRX

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EF [auth H], ZL [auth h](3R)-beta,beta-caroten-3-ol
C40 H56 O
DMASLKHVQRHNES-FKKUPVFPSA-N
 Ligand Interaction
BCR (Subject of Investigation/LOI)
Query on BCR

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CK [auth c] , DK [auth c] , JD [auth C] , JL [auth d] , KD [auth C] , KM [auth k] , NE [auth D] , PH [auth a] , 
CK [auth c], DK [auth c], JD [auth C], JL [auth d], KD [auth C], KM [auth k], NE [auth D], PH [auth a], QF [auth K], SA [auth A], TI [auth b], UI [auth b], VI [auth b], VN [auth y], WB [auth B], XB [auth B], YB [auth B], ZG [auth Y]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
LMT (Subject of Investigation/LOI)
Query on LMT

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AC [auth B] , AN [auth t] , BF [auth E] , BH [auth Z] , IF [auth I] , IK [auth c] , JG [auth T] , SK [auth c] , 
AC [auth B], AN [auth t], BF [auth E], BH [auth Z], IF [auth I], IK [auth c], JG [auth T], SK [auth c], VH [auth a], XA [auth A], XL [auth f]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
OEX (Subject of Investigation/LOI)
Query on OEX

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FH [auth a], KA [auth A]CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
 Ligand Interaction
HTG (Subject of Investigation/LOI)
Query on HTG

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AE [auth C] , BC [auth B] , BJ [auth b] , CJ [auth b] , EC [auth B] , FC [auth B] , HJ [auth b] , JK [auth c] , 
AE [auth C], BC [auth B], BJ [auth b], CJ [auth b], EC [auth B], FC [auth B], HJ [auth b], JK [auth c], MN [auth v], PD [auth C], PG [auth V], RD [auth C], RM [auth l], WE [auth D], XE [auth D], YI [auth b], ZI [auth b]
heptyl 1-thio-beta-D-glucopyranoside
C13 H26 O5 S
HPEGNLMTTNTJSP-LBELIVKGSA-N
 Ligand Interaction
DMS
Query on DMS

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AB [auth A] , AF [auth D] , AG [auth O] , AI [auth a] , AL [auth c] , BB [auth A] , BE [auth C] , BG [auth O] , 
AB [auth A], AF [auth D], AG [auth O], AI [auth a], AL [auth c], BB [auth A], BE [auth C], BG [auth O], BI [auth a], BL [auth c], CB [auth A], CE [auth C], CG [auth O], CL [auth c], CN [auth t], DB [auth A], DE [auth C], DF [auth F], DG [auth O], DH [auth a], DL [auth c], DN [auth t], EE [auth C], EG [auth O], EH [auth a], EJ [auth b], EL [auth c], EN [auth t], FE [auth C], FG [auth O], FJ [auth b], FL [auth c], GC [auth B], GE [auth C], GF [auth H], GG [auth O], GJ [auth b], GM [auth i], GN [auth u], HC [auth B], HE [auth C], HF [auth I], HG [auth O], HN [auth u], IC [auth B], IE [auth C], IJ [auth b], IN [auth u], JC [auth B], JJ [auth b], JN [auth u], KC [auth B], KJ [auth b], KK [auth c], KN [auth v], LC [auth B], LG [auth U], LJ [auth b], LK [auth c], MC [auth B], MF [auth I], MG [auth U], MJ [auth b], MK [auth c], NC [auth B], NG [auth V], NJ [auth b], NK [auth c], NN [auth v], OC [auth B], OK [auth c], OM [auth l], ON [auth v], PC [auth B], PK [auth c], PM [auth l], PN [auth v], QC [auth B], QG [auth V], QK [auth c], QL [auth d], QM [auth l], QN [auth v], RC [auth B], RG [auth V], RL [auth d], RN [auth v], SC [auth B], SD [auth C], SG [auth V], SL [auth d], SN [auth v], TC [auth B], TD [auth C], TF [auth L], TG [auth V], TL [auth d], TM [auth o], TN [auth v], UC [auth B], UD [auth C], UG [auth V], UK [auth c], UL [auth d], UM [auth o], UN [auth v], VD [auth C], VG [auth V], VK [auth c], VM [auth o], WD [auth C], WF [auth O], WG [auth V], WK [auth c], WM [auth o], XD [auth C], XF [auth O], XG [auth V], XH [auth a], XK [auth c], XM [auth o], YD [auth C], YE [auth D], YF [auth O], YG [auth V], YK [auth c], YL [auth f], YM [auth o], ZA [auth A], ZE [auth D], ZF [auth O], ZK [auth c], ZM [auth o]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
BCT
Query on BCT

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

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

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CI [auth b], FB [auth B], OJ [auth c], SM [auth o], VF [auth O]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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HH [auth a], IH [auth a], MA [auth A], NA [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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IM [auth j], LM [auth k], OF [auth J], RF [auth K]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
UNL
Query on UNL

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AH [auth X] , AJ [auth b] , BN [auth t] , CC [auth B] , CH [auth Z] , CM [auth i] , DC [auth B] , DJ [auth b] , 
AH [auth X], AJ [auth b], BN [auth t], CC [auth B], CH [auth Z], CM [auth i], DC [auth B], DJ [auth b], DM [auth i], EM [auth i], FM [auth i], FN [auth u], IG [auth T], JF [auth I], JM [auth j], KF [auth I], KG [auth U], LF [auth I], PF [auth J], PL [auth d], TH [auth a], TK [auth c], UF [auth O], VE [auth D], WH [auth a], WN [auth x], YA [auth A]
Unknown ligand
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME
H [auth I], Z [auth i]L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.954α = 90
b = 226.993β = 90
c = 285.886γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
XSCALEdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
JSPS KAKENHI GrantsJapan24227002
Grant-in-Aid for Scientific Research on Innovative Areas Artificial photosynthesis (AnApple)Japan24107003

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-22
    Type: Initial release
  • Version 1.1: 2017-08-30
    Changes: Data collection, Database references
  • Version 2.0: 2019-10-02
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Derived calculations, Structure summary