6JLL

XFEL structure of cyanobacterial photosystem II (2F state, dataset1)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.158 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history. 


Literature

An oxyl/oxo mechanism for oxygen-oxygen coupling in PSII revealed by an x-ray free-electron laser.

Suga, M., Akita, F., Yamashita, K., Nakajima, Y., Ueno, G., Li, H., Yamane, T., Hirata, K., Umena, Y., Yonekura, S., Yu, L.J., Murakami, H., Nomura, T., Kimura, T., Kubo, M., Baba, S., Kumasaka, T., Tono, K., Yabashi, M., Isobe, H., Yamaguchi, K., Yamamoto, M., Ago, H., Shen, J.R.

(2019) Science 366: 334-338

  • DOI: https://doi.org/10.1126/science.aax6998
  • Primary Citation of Related Structures:  
    6JLJ, 6JLK, 6JLL, 6JLM, 6JLN, 6JLO, 6JLP

  • PubMed Abstract: 

    Photosynthetic water oxidation is catalyzed by the Mn 4 CaO 5 cluster of photosystem II (PSII) with linear progression through five S-state intermediates (S 0 to S 4 ). To reveal the mechanism of water oxidation, we analyzed structures of PSII in the S 1 , S 2 , and S 3 states by x-ray free-electron laser serial crystallography. No insertion of water was found in S 2 , but flipping of D1 Glu 189 upon transition to S 3 leads to the opening of a water channel and provides a space for incorporation of an additional oxygen ligand, resulting in an open cubane Mn 4 CaO 6 cluster with an oxyl/oxo bridge. Structural changes of PSII between the different S states reveal cooperative action of substrate water access, proton release, and dioxygen formation in photosynthetic water oxidation.

    • Organizational Affiliation: 

    Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima Naka, Okayama 700-8530, Japan. michisuga@okayama-u.ac.jp ago@spring8.or.jp shen@cc.okayama-u.ac.jp.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II protein D1A,
U [auth a]		344Thermostichus vulcanusMutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
Find proteins for P51765 (Thermostichus vulcanus)
Explore P51765 
Go to UniProtKB:  P51765
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51765
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinB,
V [auth b]		505Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0VWR1 (Thermostichus vulcanus)
Explore D0VWR1 
Go to UniProtKB:  D0VWR1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0VWR1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinC,
W [auth c]		455Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0VWR7 (Thermostichus vulcanus)
Explore D0VWR7 
Go to UniProtKB:  D0VWR7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0VWR7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinD,
X [auth d]		342Thermostichus vulcanusMutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
Find proteins for D0VWR8 (Thermostichus vulcanus)
Explore D0VWR8 
Go to UniProtKB:  D0VWR8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0VWR8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaE,
Y [auth e]		84Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P12238 (Thermostichus vulcanus)
Explore P12238 
Go to UniProtKB:  P12238
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12238
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaF,
Z [auth f]		44Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P12239 (Thermostichus vulcanus)
Explore P12239 
Go to UniProtKB:  P12239
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12239
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HAA [auth h],
G [auth H]		65Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P19052 (Thermostichus vulcanus)
Explore P19052 
Go to UniProtKB:  P19052
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19052
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein IBA [auth i],
H [auth I]		38Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P12240 (Thermostichus vulcanus)
Explore P12240 
Go to UniProtKB:  P12240
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12240
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein JCA [auth j],
I [auth J]		39Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q7DGD4 (Thermostichus vulcanus)
Explore Q7DGD4 
Go to UniProtKB:  Q7DGD4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7DGD4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KDA [auth k],
J [auth K]		37Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P19054 (Thermostichus vulcanus)
Explore P19054 
Go to UniProtKB:  P19054
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19054
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LEA [auth l],
K [auth L]		37Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P12241 (Thermostichus vulcanus)
Explore P12241 
Go to UniProtKB:  P12241
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12241
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein MFA [auth m],
L [auth M]		36Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P12312 (Thermostichus vulcanus)
Explore P12312 
Go to UniProtKB:  P12312
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12312
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II manganese-stabilizing polypeptideGA [auth o],
M [auth O]		244Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0VWR2 (Thermostichus vulcanus)
Explore D0VWR2 
Go to UniProtKB:  D0VWR2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0VWR2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein THA [auth t],
N [auth T]		32Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P12313 (Thermostichus vulcanus)
Explore P12313 
Go to UniProtKB:  P12313
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12313
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II 12 kDa extrinsic proteinIA [auth u],
O [auth U]		104Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P56152 (Thermostichus vulcanus)
Explore P56152 
Go to UniProtKB:  P56152
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56152
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c-550JA [auth v],
P [auth V]		137Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0A387 (Thermostichus vulcanus)
Explore P0A387 
Go to UniProtKB:  P0A387
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A387
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12KA [auth y],
Q [auth Y]		30Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0VWR3 (Thermostichus vulcanus)
Explore D0VWR3 
Go to UniProtKB:  D0VWR3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0VWR3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein XLA [auth x],
R [auth X]		40Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0VWR4 (Thermostichus vulcanus)
Explore D0VWR4 
Go to UniProtKB:  D0VWR4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0VWR4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZMA [auth z],
S [auth Z]		62Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0VWR5 (Thermostichus vulcanus)
Explore D0VWR5 
Go to UniProtKB:  D0VWR5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0VWR5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II protein YT [auth R]34Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0DM37 (Thermostichus vulcanus)
Explore P0DM37 
Go to UniProtKB:  P0DM37
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DM37
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 20 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD
Download Ideal Coordinates CCD File 
FJ [auth e]
ID [auth C]
JD [auth C]
KD [auth C]
KI [auth c]
FJ [auth e],
ID [auth C],
JD [auth C],
KD [auth C],
KI [auth c],
LI [auth c],
MI [auth c],
MJ [auth h],
NE [auth H],
ZD [auth D]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA
Query on CLA
Download Ideal Coordinates CCD File 
AD [auth C]
AH [auth b]
AI [auth c]
BD [auth C]
BH [auth b]
AD [auth C],
AH [auth b],
AI [auth c],
BD [auth C],
BH [auth b],
BI [auth c],
CD [auth C],
CH [auth b],
CI [auth c],
DD [auth C],
DH [auth b],
DI [auth c],
ED [auth C],
EH [auth b],
EI [auth c],
FD [auth C],
FH [auth b],
FI [auth c],
GH [auth b],
GI [auth c],
HH [auth b],
HI [auth c],
IH [auth b],
II [auth c],
JH [auth b],
KB [auth B],
LB [auth B],
MB [auth B],
NB [auth B],
OB [auth B],
PB [auth B],
QB [auth B],
RA [auth A],
RB [auth B],
SA [auth A],
SB [auth B],
TA [auth A],
TB [auth B],
TC [auth C],
TI [auth d],
UB [auth B],
UC [auth C],
UG [auth b],
UI [auth d],
VB [auth B],
VC [auth C],
VD [auth D],
VG [auth b],
VI [auth d],
WA [auth A],
WB [auth B],
WC [auth C],
WD [auth D],
WF [auth a],
WG [auth b],
WH [auth c],
XB [auth B],
XC [auth C],
XF [auth a],
XG [auth b],
XH [auth c],
YB [auth B],
YC [auth C],
YG [auth b],
YH [auth c],
ZB [auth B],
ZC [auth C],
ZF [auth a],
ZG [auth b],
ZH [auth c]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO
Query on PHO
Download Ideal Coordinates CCD File 
HG [auth a],
UA [auth A],
VA [auth A],
YF [auth a]		PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD
Query on SQD
Download Ideal Coordinates CCD File 
BG [auth a]
CB [auth A]
DC [auth B]
IJ [auth f]
JE [auth F]
BG [auth a],
CB [auth A],
DC [auth B],
IJ [auth f],
JE [auth F],
KG [auth b],
SF [auth a],
YA [auth A]
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG
Query on LMG
Download Ideal Coordinates CCD File 
CG [auth a]
EC [auth B]
FE [auth D]
FK [auth z]
IB [auth A]
CG [auth a],
EC [auth B],
FE [auth D],
FK [auth z],
IB [auth A],
LD [auth C],
MD [auth C],
NF [auth Z],
NH [auth b],
NI [auth c],
OI [auth c],
OJ [auth j]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9
Query on PL9
Download Ideal Coordinates CCD File 
DG [auth a],
GB [auth A],
XI [auth d],
YD [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
LHG
Query on LHG
Download Ideal Coordinates CCD File 
AE [auth D]
AJ [auth d]
BE [auth D]
CE [auth D]
GE [auth E]
AE [auth D],
AJ [auth d],
BE [auth D],
CE [auth D],
GE [auth E],
JG [auth a],
SE [auth L],
SJ [auth l],
YI [auth d],
ZI [auth d]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEM
Query on HEM
Download Ideal Coordinates CCD File 
DK [auth v],
GJ [auth e],
IE [auth F],
JF [auth V]		PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
BCR
Query on BCR
Download Ideal Coordinates CCD File 
AC [auth B]
AG [auth a]
BC [auth B]
BF [auth T]
CC [auth B]
AC [auth B],
AG [auth a],
BC [auth B],
BF [auth T],
CC [auth B],
EK [auth y],
GD [auth C],
HD [auth C],
JI [auth c],
KH [auth b],
LF [auth Y],
LH [auth b],
LJ [auth h],
ME [auth H],
MH [auth b],
RE [auth K],
RJ [auth k],
SI [auth c],
WI [auth d],
XA [auth A],
XD [auth D],
XJ [auth t]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
Query on LMT
Download Ideal Coordinates CCD File 
CF [auth T]
DB [auth A]
HE [auth F]
IG [auth a]
JJ [auth f]
CF [auth T],
DB [auth A],
HE [auth F],
IG [auth a],
JJ [auth f],
ND [auth C],
OH [auth b],
RC [auth B],
RF [auth a],
TE [auth M],
UD [auth D],
UJ [auth m],
VE [auth M],
WE [auth M]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
OEY
Query on OEY
Download Ideal Coordinates CCD File 
FB [auth A],
FG [auth a]		CA-MN4-O6 CLUSTER
Ca Mn4 O6
VXLJVOKMVCJEPF-UHFFFAOYSA-N
OEX
Query on OEX
Download Ideal Coordinates CCD File 
EB [auth A],
EG [auth a]		CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
HTG
Query on HTG
Download Ideal Coordinates CCD File 
DJ [auth d]
FC [auth B]
GC [auth B]
HC [auth B]
KF [auth V]
DJ [auth d],
FC [auth B],
GC [auth B],
HC [auth B],
KF [auth V],
LE [auth H],
LG [auth b],
OC [auth B],
OD [auth C],
PC [auth B],
PD [auth C],
PH [auth b],
PI [auth c],
QH [auth b],
QI [auth c],
RG [auth b],
SG [auth b]
heptyl 1-thio-beta-D-glucopyranoside
C13 H26 O5 S
HPEGNLMTTNTJSP-LBELIVKGSA-N
GOL
Query on GOL
Download Ideal Coordinates CCD File 
AB [auth A]
AF [auth T]
AK [auth v]
BB [auth A]
BK [auth v]
AB [auth A],
AF [auth T],
AK [auth v],
BB [auth A],
BK [auth v],
EF [auth V],
FF [auth V],
GF [auth V],
HF [auth V],
HJ [auth f],
IC [auth B],
IF [auth V],
JC [auth B],
KC [auth B],
LC [auth B],
MC [auth B],
MG [auth b],
NC [auth B],
NG [auth b],
OF [auth a],
OG [auth b],
PF [auth a],
PG [auth b],
QD [auth C],
QG [auth b],
RD [auth C],
SC [auth B],
SH [auth c],
TH [auth c],
VJ [auth o],
XE [auth O],
YJ [auth t],
ZA [auth A],
ZE [auth T],
ZJ [auth v]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
BCT
Query on BCT
Download Ideal Coordinates CCD File 
GG [auth a],
QA [auth A]		BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2
Query on FE2
Download Ideal Coordinates CCD File 
NA [auth A],
TF [auth a]		FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CA
Query on CA
Download Ideal Coordinates CCD File 
JB [auth B]
KE [auth F]
KJ [auth f]
SD [auth C]
TG [auth b]
JB [auth B],
KE [auth F],
KJ [auth f],
SD [auth C],
TG [auth b],
UH [auth c],
VH [auth c],
WJ [auth o],
YE [auth O]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL
Download Ideal Coordinates CCD File 
CK [auth v]
DF [auth U]
OA [auth A]
PA [auth A]
UF [auth a]
CK [auth v],
DF [auth U],
OA [auth A],
PA [auth A],
UF [auth a],
VF [auth a]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG
Download Ideal Coordinates CCD File 
QE [auth J],
QJ [auth j]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
UNL
Query on UNL
Download Ideal Coordinates CCD File 
BJ [auth d]
CJ [auth d]
DE [auth D]
EE [auth D]
EJ [auth d]
BJ [auth d],
CJ [auth d],
DE [auth D],
EE [auth D],
EJ [auth d],
HB [auth A],
MF [auth X],
NJ [auth i],
OE [auth I],
PE [auth J],
PJ [auth j],
QC [auth B],
QF [auth a],
RH [auth b],
RI [auth c],
TD [auth C],
TJ [auth m],
UE [auth M]
Unknown ligand
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D 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: 2.15 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.158 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.97α = 90
b = 228.72β = 90
c = 286.98γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan--

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-16
    Type: Initial release
  • Version 1.1: 2019-10-30
    Changes: Data collection, Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Derived calculations, Structure summary
  • Version 2.0: 2023-11-22
    Changes: Advisory, Data collection, Database references, Non-polymer description, Refinement description, Structure summary
  • Version 2.1: 2024-10-23
    Changes: Structure summary