5H2F Photosynthesis date Oct 15, 2016
title Crystal Structure Of The Psbm-Deletion Mutant Of Photosystem
authors S.Uto, K.Kawakami, Y.Umena, M.Iwai, M.Ikeuchi, J.R.Shen, N.Kamiya
compound source
Molecule: Photosystem II Protein D1 1
Chain: A, a
Fragment: Unp Residues 11-344
Synonym: Psii D1 Protein 1,Photosystem II Q(B) Protein 1
Ec: 1.10.3.9
Organism_scientific: Thermosynechococcus Elongatus (Strain
Organism_taxid: 197221
Strain: Bp-1

Molecule: Photosystem II Cp47 Reaction Center Protein
Chain: B, b
Fragment: Unp Residues 2-506
Synonym: Psii 47 Kda Protein,Protein Cp-47

Organism_scientific: Thermosynechococcus Elongatus
Organism_taxid: 197221
Strain: Bp-1

Molecule: Photosystem II Cp43 Reaction Center Protein
Chain: C, c
Fragment: Unp Residues 7-461
Synonym: Psii 43 Kda Protein,Protein Cp-43

Organism_scientific: Thermosynechococcus Elongatus (Strain
Organism_taxid: 197221
Strain: Bp-1

Molecule: Photosystem II D2 Protein
Chain: D, d
Fragment: Unp Residues 11-352
Synonym: Psii D2 Protein,Photosystem II Q(A) Protein
Ec: 1.10.3.9

Organism_scientific: Thermosynechococcus Elongatus (Strain
Organism_taxid: 197221
Strain: Bp-1

Molecule: Cytochrome B559 Subunit Alpha
Chain: E, e
Fragment: Unp Residues 5-84
Synonym: Psii Reaction Center Subunit V

Organism_scientific: Thermosynechococcus Elongatus
Organism_taxid: 197221
Strain: Bp-1

Molecule: Cytochrome B559 Subunit Beta
Chain: F, f
Fragment: Unp Residues 13-45
Synonym: Psii Reaction Center Subunit Vi

Organism_scientific: Thermosynechococcus Elongatus (Strain
Organism_taxid: 197221
Strain: Bp-1

Molecule: Photosystem II Reaction Center Protein H
Chain: H, h
Fragment: Unp Residues 2-64
Synonym: Psii-H

Organism_scientific: Thermosynechococcus Elongatus (Strain
Organism_taxid: 197221
Strain: Bp-1

Molecule: Photosystem II Reaction Center Protein I
Chain: I, I
Fragment: Unp Residues 1-36
Synonym: Psii-I,Psii 4.4 Kda Protein

Organism_scientific: Thermosynechococcus Elongatus
Organism_taxid: 197221
Strain: Bp-1

Molecule: Photosystem II Reaction Center Protein J
Chain: J, j
Fragment: Unp Residues 1-40
Synonym: Psii-J

Organism_scientific: Thermosynechococcus Elongatus
Organism_taxid: 197221
Strain: Bp-1

Molecule: Photosystem II Reaction Center Protein K
Chain: K, k
Synonym: Psii-K

Organism_scientific: Thermosynechococcus Elongatus (Strain
Organism_taxid: 197221
Strain: Bp-1

Molecule: Photosystem II Reaction Center Protein L
Chain: L, l
Fragment: Unp Residues 3-37
Synonym: Psii-L

Organism_scientific: Thermosynechococcus Elongatus (Strain
Organism_taxid: 197221
Strain: Bp-1

Molecule: Photosystem II Manganese-Stabilizing Polypeptide
Chain: O, o
Fragment: Unp Residues 30-272
Synonym: Msp

Organism_scientific: Thermosynechococcus Elongatus (Strain
Organism_taxid: 197221
Strain: Bp-1

Molecule: Photosystem II Reaction Center Protein T
Chain: T, t
Fragment: Unp Residues 1-30
Synonym: Psii-Tc

Organism_scientific: Thermosynechococcus Elongatus
Organism_taxid: 197221
Strain: Bp-1

Molecule: Photosystem II 12 Kda Extrinsic Protein
Chain: U, u
Fragment: Unp Residues 38-134
Synonym: Ps II Complex 12 Kda Extrinsic Protein,Psii-U

Organism_scientific: Thermosynechococcus Elongatus (Strain
Organism_taxid: 197221
Strain: Bp-1

Molecule: Cytochrome C-550
Chain: V, v
Synonym: Cytochrome C-549,Cytochrome C550,Low-Potential Cyt

Organism_scientific: Thermosynechococcus Elongatus (Strain
Organism_taxid: 197221
Strain: Bp-1

Molecule: Photosystem II Reaction Center Protein Ycf12
Chain: Y, y
Fragment: Unp Residues 18-46

Organism_scientific: Thermosynechococcus Elongatus (Strain
Organism_taxid: 197221
Strain: Bp-1

Molecule: Photosystem II Reaction Center X Protein
Chain: X, x
Fragment: Unp Residues 2-38

Organism_scientific: Thermosynechococcus Elongatus (Strain
Organism_taxid: 197221
Strain: Bp-1

Molecule: Photosystem II Reaction Center Protein Z
Chain: Z, z
Synonym: Psii-Z

Organism_scientific: Thermosynechococcus Elongatus (Strain
Organism_taxid: 197221
Strain: Bp-1
symmetry Space Group: P 21 21 21
R_factor 0.174 R_Free 0.226
crystal
cell
length a length b length c angle alpha angle beta angle gamma
121.954 226.993 285.886 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.20 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


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 referenceMutual relationships between structural and functional changes in a PsbM-deletion mutant of photosystem II., Uto S, Kawakami K, Umena Y, Iwai M, Ikeuchi M, Shen JR, Kamiya N, Faraday Discuss. 2017 Mar 8. doi: 10.1039/c6fd00213g. PMID:28272640
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1133 Kb) [Save to disk]
  • Biological Unit Coordinates (5h2f.pdb1.gz) 544 Kb
  • Biological Unit Coordinates (5h2f.pdb2.gz) 539 Kb
  • LPC: Ligand-Protein Contacts for 5H2F
  • CSU: Contacts of Structural Units for 5H2F
  • Structure Factors (26678 Kb)
  • Retrieve 5H2F in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5H2F from S2C, [Save to disk]
  • Re-refined 5h2f structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5H2F 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 5H2F
  • 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 5h2f from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5h2f_D] [5h2f_K] [5h2f_O] [5h2f_A] [5h2f_b] [5h2f_f] [5h2f_k] [5h2f_z] [5h2f_Y] [5h2f_o] [5h2f_u] [5h2f_U] [5h2f_L] [5h2f_h] [5h2f] [5h2f_C] [5h2f_a] [5h2f_v] [5h2f_J] [5h2f_V] [5h2f_y] [5h2f_X] [5h2f_j] [5h2f_c] [5h2f_l] [5h2f_E] [5h2f_H] [5h2f_Z] [5h2f_d] [5h2f_e] [5h2f_i] [5h2f_B] [5h2f_t] [5h2f_T] [5h2f_I] [5h2f_F] [5h2f_x]
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