5B5E Electron Transport, Photosynthesis date May 02, 2016
title Crystal Structure Analysis Of Photosystem II Complex
authors A.Tanaka, Y.Fukushima, N.Kamiya
compound source
Molecule: Photosystem II Protein D1
Chain: A, a
Synonym: Psii D1 Protein,Photosystem II Q(B) Protein
Ec: 1.10.3.9
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 Reaction Center Protein
Chain: C, c
Synonym: Psii 43 Kda Protein,Protein Cp-43

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
Other_details: Fme 1 (Modified Residue: N-Formylmethionine)

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 Reaction Center Protein K
Chain: K, k
Synonym: Psii-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 Reaction Center Protein M
Chain: M, m
Synonym: Psii-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
Other_details: Fme 1 (Modified Residue: N-Formylmethionine)

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 Ycf12
Chain: Y, y

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 Z
Chain: Z, z
Synonym: Psii-Z

Organism_scientific: Thermosynechococcus Vulcanus
Organism_taxid: 32053
symmetry Space Group: P 21 21 21
R_factor 0.171 R_Free 0.212
crystal
cell
length a length b length c angle alpha angle beta angle gamma
121.404 228.224 286.429 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.87 Å
ligand BCR, BCT, CA, CL, CLA, DGD, DMS, FE2, FME, HEC, HEM, HTG, LHG, LMG, LMT, MG, OEX, PHO, PL9, RRX, 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


  • T, t


    Y, y


    Z, z


    a, A


    c, C


    d, D


    j, J


    u, U


    v, V


    x, X


    Primary referenceTwo Different Structures of the Oxygen-Evolving Complex in the Same Polypeptide Frameworks of Photosystem II., Tanaka A, Fukushima Y, Kamiya N, J Am Chem Soc. 2017 Jan 30. doi: 10.1021/jacs.6b09666. PMID:28102667
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1159 Kb) [Save to disk]
  • Biological Unit Coordinates (5b5e.pdb1.gz) 1084 Kb
  • LPC: Ligand-Protein Contacts for 5B5E
  • CSU: Contacts of Structural Units for 5B5E
  • Structure Factors (13837 Kb)
  • Retrieve 5B5E in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5B5E from S2C, [Save to disk]
  • Re-refined 5b5e structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
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  • Proteopedia, because life has more than 2D.
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  • 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: [5b5e_t] [5b5e_C] [5b5e_L] [5b5e_A] [5b5e_b] [5b5e_F] [5b5e_o] [5b5e] [5b5e_x] [5b5e_K] [5b5e_v] [5b5e_a] [5b5e_u] [5b5e_d] [5b5e_h] [5b5e_Z] [5b5e_z] [5b5e_D] [5b5e_M] [5b5e_V] [5b5e_y] [5b5e_B] [5b5e_m] [5b5e_I] [5b5e_J] [5b5e_U] [5b5e_T] [5b5e_H] [5b5e_l] [5b5e_O] [5b5e_k] [5b5e_Y] [5b5e_f] [5b5e_X] [5b5e_e] [5b5e_c] [5b5e_j] [5b5e_i] [5b5e_E]
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