5ZZN

Crystal structure of photosystem II from an SQDG-deficient mutant of Thermosynechococcus elongatus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.156 

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Thylakoid membrane lipid sulfoquinovosyl-diacylglycerol (SQDG) is required for full functioning of photosystem II inThermosynechococcus elongatus.

Nakajima, Y.Umena, Y.Nagao, R.Endo, K.Kobayashi, K.Akita, F.Suga, M.Wada, H.Noguchi, T.Shen, J.R.

(2018) J Biol Chem 293: 14786-14797

  • DOI: 10.1074/jbc.RA118.004304
  • Primary Citation of Related Structures:  
    5ZZN

  • PubMed Abstract: 
  • Sulfoquinovosyl-diacylglycerol (SQDG) is one of the four lipids present in the thylakoid membranes. Depletion of SQDG causes different degrees of effects on photosynthetic growth and activities in different organisms. Four SQDG molecules bind to each monomer of photosystem II (PSII), but their role in PSII function has not been characterized in detail, and no PSII structure without SQDG has been reported ...

    Sulfoquinovosyl-diacylglycerol (SQDG) is one of the four lipids present in the thylakoid membranes. Depletion of SQDG causes different degrees of effects on photosynthetic growth and activities in different organisms. Four SQDG molecules bind to each monomer of photosystem II (PSII), but their role in PSII function has not been characterized in detail, and no PSII structure without SQDG has been reported. We analyzed the activities of PSII from an SQDG-deficient mutant of the cyanobacterium Thermosynechococcus elongatus by various spectroscopic methods, which showed that depletion of SQDG partially impaired the PSII activity by impairing secondary quinone (Q B ) exchange at the acceptor site. We further solved the crystal structure of the PSII dimer from the SQDG deletion mutant at 2.1 Å resolution and found that all of the four SQDG-binding sites were occupied by other lipids, most likely PG molecules. Replacement of SQDG at a site near the head of Q B provides a possible explanation for the Q B impairment. The replacement of two SQDGs located at the monomer-monomer interface by other lipids decreased the stability of the PSII dimer, resulting in an increase in the amount of PSII monomer in the mutant. The present results thus suggest that although SQDG binding in all of the PSII-binding sites is necessary to fully maintain the activity and stability of PSII, replacement of SQDG by other lipids can partially compensate for their functions.


    Organizational Affiliation

    From the Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530, shen@cc.okayama-u.ac.jp.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem II protein D1 1A, T [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, U [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, V [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, W [auth d]342Thermosynechococcus 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]81Thermosynechococcus 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]34Thermosynechococcus 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], Z [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], AA [auth i]37Thermosynechococcus 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], 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]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], DA [auth l]36Thermosynechococcus 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]34Thermosynechococcus 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]243Thermosynechococcus 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], GA [auth t]30Thermosynechococcus 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], HA [auth u]97Thermosynechococcus 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], IA [auth v]137Thermosynechococcus 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], JA [auth y]29Thermosynechococcus 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], KA [auth x]39Thermosynechococcus 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], LA [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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DM [auth h] , GK [auth c] , HK [auth c] , IK [auth c] , JF [auth H] , MD [auth C] , ML [auth d] , ND [auth C] , 
DM [auth h], GK [auth c], HK [auth c], IK [auth c], JF [auth H], MD [auth C], ML [auth d], ND [auth C], OD [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] , CK [auth c] , DD [auth C] , DK [auth c] , 
AD [auth C], AK [auth c], BD [auth C], BK [auth c], CD [auth C], CK [auth c], DD [auth C], DK [auth c], ED [auth C], FD [auth C], FI [auth b], GD [auth C], GI [auth b], GL [auth d], HD [auth C], HI [auth b], HL [auth d], IB [auth B], ID [auth C], II [auth b], JB [auth B], JD [auth C], JI [auth b], JL [auth d], KB [auth B], KD [auth C], KE [auth D], KI [auth b], LB [auth B], LH [auth a], LI [auth b], MB [auth B], ME [auth D], MH [auth a], MI [auth b], NB [auth B], NI [auth b], OB [auth B], OH [auth a], OI [auth b], PA [auth A], PB [auth B], PI [auth b], QA [auth A], QB [auth B], QI [auth b], RA [auth A], RB [auth B], RI [auth b], RJ [auth c], SB [auth B], SI [auth b], SJ [auth c], TA [auth A], TB [auth B], TI [auth b], TJ [auth c], UB [auth B], UI [auth b], UJ [auth c], VB [auth B], VJ [auth c], WB [auth B], WJ [auth c], XB [auth B], 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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IL [auth d], LE [auth D], NH [auth a], SA [auth A]PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
 Ligand Interaction
LMG (Subject of Investigation/LOI)
Query on LMG

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CC [auth B] , JK [auth c] , KK [auth c] , PD [auth C] , QD [auth C] , QL [auth d] , RH [auth a] , TE [auth D] , 
CC [auth B], JK [auth c], KK [auth c], PD [auth C], QD [auth C], QL [auth d], RH [auth a], TE [auth D], WA [auth A], ZI [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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LL [auth d], OE [auth D], QH [auth a], VA [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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BC [auth B] , CF [auth E] , CM [auth f] , IF [auth F] , NL [auth d] , OL [auth d] , PL [auth d] , QE [auth D] , 
BC [auth B], CF [auth E], CM [auth f], IF [auth F], NL [auth d], OL [auth d], PL [auth d], QE [auth D], RE [auth D], SE [auth D], WL [auth e], YI [auth b]
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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ON [auth v], TG [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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BM [auth f], GF [auth F]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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EM [auth h], KF [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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AC [auth B] , CH [auth Y] , EK [auth c] , FK [auth c] , GN [auth t] , KL [auth d] , LD [auth C] , NE [auth D] , 
AC [auth B], CH [auth Y], EK [auth c], FK [auth c], GN [auth t], KL [auth d], LD [auth C], NE [auth D], NG [auth T], PH [auth a], PM [auth k], UA [auth A], VF [auth K], VI [auth b], WF [auth K], WI [auth b], WN [auth y], XI [auth b], YB [auth B], ZB [auth B]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
LMT (Subject of Investigation/LOI)
Query on LMT

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AB [auth A] , AG [auth M] , AJ [auth b] , DC [auth B] , EH [auth Z] , GH [auth a] , HF [auth F] , HN [auth t] , 
AB [auth A], AG [auth M], AJ [auth b], DC [auth B], EH [auth Z], GH [auth a], HF [auth F], HN [auth t], LK [auth c], MM [auth j], OG [auth T], RD [auth C], RM [auth l], SM [auth m], TF [auth J], TM [auth m], UM [auth m], YN [auth z], ZF [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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HH [auth a], MA [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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BI [auth b] , BJ [auth b] , CG [auth O] , CI [auth b] , EC [auth B] , EL [auth c] , GE [auth C] , HE [auth C] , 
BI [auth b], BJ [auth b], CG [auth O], CI [auth b], EC [auth B], EL [auth c], GE [auth C], HE [auth C], IC [auth B], JC [auth B], MK [auth c], NK [auth c], OJ [auth b], RL [auth d], SD [auth C], SG [auth U], TD [auth C], UE [auth D], UG [auth V], UN [auth v], VM [auth o], WC [auth B]
heptyl 1-thio-beta-D-glucopyranoside
C13 H26 O5 S
HPEGNLMTTNTJSP-LBELIVKGSA-N
 Ligand Interaction
GOL
Query on GOL

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EE [auth C], KJ [auth b], WK [auth c], YE [auth D], ZL [auth e]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

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AE [auth C] , AF [auth D] , AH [auth V] , AL [auth c] , AM [auth e] , AN [auth o] , BB [auth A] , BE [auth C] , 
AE [auth C], AF [auth D], AH [auth V], AL [auth c], AM [auth e], AN [auth o], BB [auth A], BE [auth C], BF [auth D], BL [auth c], BN [auth o], CB [auth A], CE [auth C], CL [auth c], CN [auth o], DB [auth A], DE [auth C], DG [auth O], DL [auth c], DN [auth o], EB [auth A], EG [auth O], EJ [auth b], EN [auth o], FE [auth C], FF [auth E], FG [auth O], FJ [auth b], FN [auth o], GG [auth O], GJ [auth b], GM [auth h], HG [auth O], HJ [auth b], IG [auth O], IJ [auth b], JG [auth O], JJ [auth b], KG [auth O], KN [auth u], LC [auth B], LG [auth O], LJ [auth b], LN [auth u], MC [auth B], MG [auth O], MJ [auth b], MN [auth u], NC [auth B], NJ [auth b], OC [auth B], PC [auth B], PN [auth v], QC [auth B], QN [auth v], RC [auth B], RF [auth I], RG [auth U], RK [auth c], RN [auth v], SC [auth B], SK [auth c], SN [auth v], TC [auth B], TK [auth c], TL [auth d], TN [auth v], UC [auth B], UK [auth c], UL [auth d], VC [auth B], VG [auth V], VH [auth a], VK [auth c], WD [auth C], WE [auth D], WG [auth V], WH [auth a], XD [auth C], XE [auth D], XG [auth V], XH [auth a], XK [auth c], XM [auth o], YD [auth C], YG [auth V], YH [auth a], YK [auth c], YM [auth o], ZD [auth C], ZE [auth D], ZG [auth V], ZH [auth a], 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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FL [auth d], JE [auth D]BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
 Ligand Interaction
FE2
Query on FE2

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

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BG [auth O], BH [auth V], EI [auth b], HB [auth B], QJ [auth c], VN [auth v], WM [auth o]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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JH [auth a], KH [auth a], NA [auth A], NN [auth v], OA [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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LM [auth j], QM [auth k], SF [auth J], YF [auth K]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
UNL
Query on UNL

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AI [auth a] , CJ [auth b] , DF [auth E] , DH [auth X] , DI [auth b] , DJ [auth b] , EF [auth E] , FB [auth A] , 
AI [auth a], CJ [auth b], DF [auth E], DH [auth X], DI [auth b], DJ [auth b], EF [auth E], FB [auth A], FC [auth B], FH [auth Z], FM [auth h], GB [auth A], GC [auth B], HC [auth B], HM [auth i], IM [auth i], IN [auth t], JM [auth i], JN [auth u], KC [auth B], KM [auth i], LF [auth H], MF [auth H], NF [auth I], NM [auth j], OF [auth I], OK [auth c], OM [auth j], PF [auth I], PG [auth T], PJ [auth b], PK [auth c], QF [auth I], QG [auth U], QK [auth c], SH [auth a], SL [auth d], TH [auth a], UD [auth C], UF [auth J], UH [auth a], VD [auth C], VE [auth D], VL [auth d], XA [auth A], XC [auth B], XF [auth K], XL [auth e], XN [auth x], YA [auth A], YL [auth e], ZA [auth A]
Unknown ligand
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
HSK
Query on HSK
D, W [auth d]L-PEPTIDE LINKINGC6 H9 N3 O3HIS
FME
Query on FME
AA [auth i], H [auth I]L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.156 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.25α = 90
b = 228.43β = 90
c = 287.12γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Cootmodel building
PDB_EXTRACTdata extraction
MOLREPphasing
XDSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapanJP17H06434
Japan Society for the Promotion of ScienceJapanJP16K21181
Japan Science and TechnologyJapanJPMJPR16P1

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-01
    Type: Initial release
  • Version 1.1: 2018-09-05
    Changes: Data collection, Database references
  • Version 1.2: 2018-10-03
    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