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 1PE, 2PE, BCR, BCT, CA, CL, CLA, DGD, EDO, FE2, FME, GOL, HEC, HEM, HTG, LHG, LMG, LMT, MG, MHS, OEX, P6G, PE8, PG4, PGE, PHO, PL9, SQD 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] (2437 Kb) [Save to disk]
  • Biological Unit Coordinates (5v2c.pdb1.gz) 2347 Kb
  • LPC: Ligand-Protein Contacts for 5V2C
  • 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
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • 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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