5V2C Electron Transport, Photosynthesis date Mar 03, 2017
title Re-Refinement Of Crystal Structure Of Photosystem II Complex
authors J.Wang, J.M.Wiwczar, G.W.Brudvig
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

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

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
Fragment: Residues 27-163
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 0.092 R_Free 0.163
crystal
cell
length a length b length c angle alpha angle beta angle gamma
122.190 228.510 286.400 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand
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 referenceChlorophyll a with a farnesyl tail in thermophilic cyanobacteria., Wiwczar JM, LaFountain AM, Wang J, Frank HA, Brudvig GW, Photosynth Res. 2017 Jul 24. doi: 10.1007/s11120-017-0425-4. PMID:28741056
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (2516 Kb) [Save to disk]
  • Biological Unit Coordinates (5v2c.pdb1.gz) 2417 Kb
  • CSU: Contacts of Structural Units for 5V2C
  • Structure Factors (9027 Kb)
  • Retrieve 5V2C in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5V2C from S2C, [Save to disk]
  • View 5V2C 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 5V2C
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5v2c from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5v2c_J] [5v2c_u] [5v2c_f] [5v2c_j] [5v2c_z] [5v2c_e] [5v2c_t] [5v2c_C] [5v2c_o] [5v2c_V] [5v2c_h] [5v2c_U] [5v2c_M] [5v2c_D] [5v2c_c] [5v2c_k] [5v2c_F] [5v2c_A] [5v2c_I] [5v2c_a] [5v2c_L] [5v2c_B] [5v2c_x] [5v2c_X] [5v2c_K] [5v2c_O] [5v2c_H] [5v2c_T] [5v2c_d] [5v2c_l] [5v2c_b] [5v2c_Z] [5v2c_E] [5v2c_i] [5v2c_y] [5v2c_Y] [5v2c_m] [5v2c_v]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5V2C
  • Community annotation for 5V2C at PDBWiki (http://pdbwiki.org)

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