5GTI Photosynthesis date Aug 20, 2016
title Native Xfel Structure Of Photosystem II (Two Flash Dataset)
authors M.Suga, J.R.Shen
compound source
Molecule: Photosystem II D1 Protein
Chain: A, a
 Organism_scientific: Thermosynechococcus Vulcanus
Organism_taxid: 32053

Molecule: Photosystem II Cp47 Reaction Center Protein
Chain: B, b
Synonym: Psii 47 Kda Protein,Protein Cp-47
Organism_scientific: Thermosynechococcus Vulcanus
Organism_taxid: 32053

Molecule: Photosystem II Cp43 Protein
Chain: C, c
Organism_scientific: Thermosynechococcus Vulcanus
Organism_taxid: 32053

Molecule: Photosystem II D2 Protein
Chain: D, d
Synonym: Psii D2 Protein,Photosystem Q(A) Protein
Ec: 1.10.3.9
Organism_scientific: Thermosynechococcus Vulcanus
Organism_taxid: 32053

Molecule: Cytochrome B559 Subunit Alpha
Chain: E, e
Synonym: Psii Reaction Center Subunit V
Organism_scientific: Thermosynechococcus Vulcanus
Organism_taxid: 32053

Molecule: Cytochrome B559 Subunit Beta
Chain: F, f
Synonym: Psii Reaction Center Subunit Vi
Organism_scientific: Thermosynechococcus Vulcanus
Organism_taxid: 32053

Molecule: Photosystem II Reaction Center Protein H
Chain: H, h
Synonym: Psii-H
Organism_scientific: Thermosynechococcus Vulcanus
Organism_taxid: 32053

Molecule: Photosystem II Reaction Center Protein I
Chain: I, I
Synonym: Psii-I,Psii 4.4 Kda Protein
Organism_scientific: Thermosynechococcus Vulcanus
Organism_taxid: 32053

Molecule: Photosystem II Reaction Center Protein J
Chain: J, j
Synonym: Psii-J
Organism_scientific: Thermosynechococcus Vulcanus
Organism_taxid: 32053

Molecule: Photosystem II Psbk Protein
Chain: K, k
Organism_scientific: Thermosynechococcus Vulcanus
Organism_taxid: 32053

Molecule: Photosystem II Reaction Center Protein L
Chain: L, l
Synonym: Psii-L
Organism_scientific: Thermosynechococcus Vulcanus
Organism_taxid: 32053

Molecule: Photosystem II Psbm Protein
Chain: M, m
Organism_scientific: Thermosynechococcus Vulcanus
Organism_taxid: 32053

Molecule: Photosystem II Manganese-Stabilizing Polypeptide
Chain: O, o
Synonym: Msp
Organism_scientific: Thermosynechococcus Vulcanus
Organism_taxid: 32053

Molecule: Photosystem II Reaction Center Protein T
Chain: T, t
Synonym: Psii-Tc
Organism_scientific: Thermosynechococcus Vulcanus
Organism_taxid: 32053

Molecule: Photosystem II 12 Kda Extrinsic Protein
Chain: U, u
Synonym: Ps II Complex 12 Kda Extrinsic Protein,Psii-U
Organism_scientific: Thermosynechococcus Vulcanus
Organism_taxid: 32053

Molecule: Cytochrome C-550
Chain: V, v
Synonym: Cytochrome C550,Low-Potential Cytochrome C
Organism_scientific: Thermosynechococcus Vulcanus
Organism_taxid: 32053

Molecule: Photosystem II Reaction Center Protein X
Chain: X, x
Organism_scientific: Thermosynechococcus Vulcanus
Organism_taxid: 32053

Molecule: Photosystem II Reaction Center Protein Ycf12
Chain: Y, y
Organism_scientific: Thermosynechococcus Vulcanus
Organism_taxid: 32053

Molecule: Photosystem II Reaction Center Protein Z
Chain: Z, z
Synonym: Psii-Z
Organism_scientific: Thermosynechococcus Vulcanus
Organism_taxid: 32053

Molecule: Photosystem II Protein Y
Chain: R
Organism_scientific: Thermosynechococcus Vulcanus
Organism_taxid: 32053
symmetry Space Group: P 21 21 21
R_factor 0.139 R_Free 0.187
crystal
cell
length a length b length c angle alpha angle beta angle gamma
126.520 231.230 287.460 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand BCR, BCT, CA, CL, CLA, DGD, FE2, FME, GOL, HEC, HEM, HTG, LHG, LMG, LMT, MG, OEX, PHO, PL9, SQD, UNL enzyme Oxidoreductase E.C.1.10.3.9 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
B, b


E, e


F, f


H, h


I, i


K, k


L, l


M, m


O, o
  • oxygen evolving activity


    • R


    T, t


    Y, y


    Z, z


    a, A


    c, C


    d, D


    j, J


    u, U


    v, V


    x, X


    Primary referenceLight-induced structural changes and the site of O=O bond formation in PSII caught by XFEL., Suga M, Akita F, Sugahara M, Kubo M, Nakajima Y, Nakane T, Yamashita K, Umena Y, Nakabayashi M, Yamane T, Nakano T, Suzuki M, Masuda T, Inoue S, Kimura T, Nomura T, Yonekura S, Yu LJ, Sakamoto T, Motomura T, Chen JH, Kato Y, Noguchi T, Tono K, Joti Y, Kameshima T, Hatsui T, Nango E, Tanaka R, Naitow H, Matsuura Y, Yamashita A, Yamamoto M, Nureki O, Yabashi M, Ishikawa T, Iwata S, Shen JR, Nature. 2017 Mar 2;543(7643):131-135. doi: 10.1038/nature21400. Epub 2017 Feb 20. PMID:28219079
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (2217 Kb) [Save to disk]
  • Biological Unit Coordinates (5gti.pdb1.gz) 1090 Kb
  • Biological Unit Coordinates (5gti.pdb2.gz) 1067 Kb
  • LPC: Ligand-Protein Contacts for 5GTI
  • CSU: Contacts of Structural Units for 5GTI
  • Structure Factors (6303 Kb)
  • Retrieve 5GTI in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5GTI from S2C, [Save to disk]
  • Re-refined 5gti structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5GTI in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 5GTI
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5gti_h] [5gti_J] [5gti_L] [5gti_x] [5gti_v] [5gti_k] [5gti_Z] [5gti_y] [5gti_T] [5gti_O] [5gti_c] [5gti_a] [5gti_z] [5gti_C] [5gti_K] [5gti_F] [5gti_Y] [5gti_i] [5gti_d] [5gti_l] [5gti_H] [5gti_M] [5gti] [5gti_f] [5gti_B] [5gti_t] [5gti_V] [5gti_o] [5gti_A] [5gti_D] [5gti_E] [5gti_j] [5gti_U] [5gti_b] [5gti_X] [5gti_u] [5gti_m] [5gti_R] [5gti_e] [5gti_I]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5GTI
  • Community annotation for 5GTI at PDBWiki (http://pdbwiki.org)

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