3A0B Electron Transport date Mar 16, 2009
title Crystal Structure Of Br-Substituted Photosystem II Complex
authors K.Kawakami, Y.Umena, N.Kamiya, J.R.Shen
compound source
Molecule: Photosystem Q(B) Protein
Chain: A, a
Synonym: 32 Kda Thylakoid Membrane Protein, Photosystem II Protein D1;
Organism_scientific: Thermosynechococcus Vulcanus
Organism_common: Synechococcus Vulcanus
Organism_taxid: 32053
Cellular_location: Thylakoid Membrane

Molecule: Photosystem II Core Light Harvesting Protein
Chain: B, b

Organism_scientific: Thermosynechococcus Vulcanus
Organism_common: Synechococcus Vulcanus
Organism_taxid: 32053
Cellular_location: Thylakoid Membrane

Molecule: Photosystem II Cp43 Protein
Chain: C, c

Organism_scientific: Thermosynechococcus Vulcanus
Organism_common: Synechococcus Vulcanus
Organism_taxid: 32053
Cellular_location: Thylakoid Membrane

Molecule: Photosystem II D2 Protein
Chain: D, d

Organism_scientific: Thermosynechococcus Vulcanus
Organism_common: Synechococcus Vulcanus
Organism_taxid: 32053
Cellular_location: Thylakoid Membrane

Molecule: Cytochrome B559 Subunit Alpha
Chain: E, e
Synonym: Psii Reaction Center Subunit V

Organism_scientific: Thermosynechococcus Vulcanus
Organism_common: Synechococcus Vulcanus
Organism_taxid: 32053
Cellular_location: Thylakoid Membrane

Molecule: Cytochrome B559 Subunit Beta
Chain: F, f
Synonym: Psii Reaction Center Subunit Vi

Organism_scientific: Thermosynechococcus Vulcanus
Organism_common: Synechococcus Vulcanus
Organism_taxid: 32053
Cellular_location: Thylakoid Membrane

Molecule: Photosystem II Reaction Center Protein H
Chain: H, h

Organism_scientific: Thermosynechococcus Vulcanus
Organism_common: Synechococcus Vulcanus
Organism_taxid: 32053
Cellular_location: Thylakoid Membrane

Molecule: Photosystem II Reaction Center Protein I
Chain: I, I

Organism_scientific: Thermosynechococcus Vulcanus
Organism_common: Synechococcus Vulcanus
Organism_taxid: 32053
Cellular_location: Thylakoid Membrane

Molecule: Photosystem II Reaction Center Protein J
Chain: J, j
Synonym: Psii-J

Organism_scientific: Thermosynechococcus Vulcanus
Organism_common: Synechococcus Vulcanus
Organism_taxid: 32053
Cellular_location: Thylakoid Membrane

Molecule: Photosystem II Reaction Center Protein K
Chain: K, k

Organism_scientific: Thermosynechococcus Vulcanus
Organism_common: Synechococcus Vulcanus
Organism_taxid: 32053
Cellular_location: Thylakoid Membrane

Molecule: Photosystem II Reaction Center Protein L
Chain: L, l
Synonym: Psii-L, Psii 5 Kda Protein

Organism_scientific: Thermosynechococcus Vulcanus
Organism_common: Synechococcus Vulcanus
Organism_taxid: 32053
Cellular_location: Thylakoid Membrane

Molecule: Photosystem II Reaction Center Protein M
Chain: M, m

Organism_scientific: Thermosynechococcus Vulcanus
Organism_common: Synechococcus Vulcanus
Organism_taxid: 32053
Cellular_location: Thylakoid Membrane

Molecule: Photosystem II Manganese-Stabilizing Polypeptide
Chain: O, o

Organism_scientific: Thermosynechococcus Vulcanus
Organism_common: Synechococcus Vulcanus
Organism_taxid: 32053
Cellular_location: Thylakoid Membrane

Molecule: Photosystem II Reaction Center Protein T
Chain: T, t
Synonym: Psii-T, Psii-Tc

Organism_scientific: Thermosynechococcus Vulcanus
Organism_common: Synechococcus Vulcanus
Organism_taxid: 32053
Cellular_location: Thylakoid Membrane

Molecule: Photosystem II 12 Kda Extrinsic Protein
Chain: U, u

Organism_scientific: Thermosynechococcus Vulcanus
Organism_common: Synechococcus Vulcanus
Organism_taxid: 32053
Cellular_location: Thylakoid Membrane

Molecule: Cytochrome C-550
Chain: V, v
Synonym: Cytochrome C550, Low-Potential Cytochrome C

Organism_scientific: Thermosynechococcus Vulcanus
Organism_common: Synechococcus Vulcanus
Organism_taxid: 32053
Cellular_location: Thylakoid Membrane

Molecule: Photosystem II Reaction Center Protein X
Chain: X, x

Organism_scientific: Thermosynechococcus Vulcanus
Organism_common: Synechococcus Vulcanus
Organism_taxid: 32053
Cellular_location: Thylakoid Membrane

Molecule: Photosystem II Reaction Center Protein Ycf12
Chain: Y, y

Organism_scientific: Thermosynechococcus Vulcanus
Organism_common: Synechococcus Vulcanus
Organism_taxid: 32053
Cellular_location: Thylakoid Membrane

Molecule: Photosystem II Reaction Center Protein Y
Chain: N, n

Organism_scientific: Thermosynechococcus Vulcanus
Organism_common: Synechococcus Vulcanus
Organism_taxid: 32053
Cellular_location: Thylakoid Membrane

Molecule: Photosystem II Reaction Center Protein Z
Chain: Z, z

Organism_scientific: Thermosynechococcus Vulcanus
Organism_common: Synechococcus Vulcanus
Organism_taxid: 32053
Cellular_location: Thylakoid Membrane
symmetry Space Group: P 21 21 21
R_factor 0.302 R_Free 0.358
crystal
cell
length a length b length c angle alpha angle beta angle gamma
130.589 226.394 307.514 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.70 Å
ligand BCR, BR, CLA, DGD, FE2, HEM, LHG, MGE, OEC, PHO, PQ9 enzyme
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 referenceLocation of chloride and its possible functions in oxygen-evolving photosystem II revealed by X-ray crystallography., Kawakami K, Umena Y, Kamiya N, Shen JR, Proc Natl Acad Sci U S A. 2009 May 26;106(21):8567-72. Epub 2009 May 11. PMID:19433803
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1036 Kb) [Save to disk]
  • Biological Unit Coordinates (3a0b.pdb1.gz) 966 Kb
  • LPC: Ligand-Protein Contacts for 3A0B
  • CSU: Contacts of Structural Units for 3A0B
  • Likely Quarternary Molecular Structure file(s) for 3A0B
  • Structure Factors (753 Kb)
  • Retrieve 3A0B in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3A0B from S2C, [Save to disk]
  • Re-refined 3a0b structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3A0B 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 3A0B
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3A0B, from MSDmotif at EBI
  • Fold representative 3a0b from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3a0b_H] [3a0b_J] [3a0b_i] [3a0b_F] [3a0b_t] [3a0b_V] [3a0b_d] [3a0b_C] [3a0b_x] [3a0b_e] [3a0b_o] [3a0b_B] [3a0b_m] [3a0b_b] [3a0b_a] [3a0b_Y] [3a0b_K] [3a0b_D] [3a0b_Z] [3a0b_n] [3a0b_f] [3a0b_A] [3a0b_I] [3a0b_M] [3a0b_l] [3a0b_c] [3a0b_y] [3a0b_k] [3a0b_X] [3a0b_h] [3a0b_v] [3a0b_z] [3a0b_O] [3a0b_E] [3a0b_U] [3a0b_N] [3a0b_j] [3a0b] [3a0b_u] [3a0b_L] [3a0b_T]
  • SWISS-PROT database: [P0A387] [D0VWR1] [D0VWR2] [D0VWR3] [D0VWR4] [D0VWR5] [D0VWR6] [D0VWR7] [D0VWR8] [D0VWR9] [P51765] [P12238] [P12239] [P12240] [Q7DGD4] [P19054] [P12241] [P12313] [P56152]
  • Domain organization of [CY550_THEVL] [D0VWR1_THEVL] [D0VWR2_THEVL] [D0VWR3_THEVL] [D0VWR4_THEVL] [D0VWR5_THEVL] [D0VWR6_THEVL] [D0VWR7_THEVL] [D0VWR8_THEVL] [D0VWR9_THEVL] [PSBA_THEVL] [PSBE_THEVL] [PSBF_THEVL] [PSBI_THEVL] [PSBJ_THEVL] [PSBK_THEVL] [PSBL_THEVL] [PSBT_THEVL] [PSBU_THEVL] by SWISSPFAM
  • Other resources with information on 3A0B
  • Community annotation for 3A0B at PDBWiki (http://pdbwiki.org)
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