1S5L Photosynthesis date Jan 21, 2004
title Architecture Of The Photosynthetic Oxygen Evolving Center
authors K.N.Ferreira, T.M.Iverson, K.Maghlaoui, J.Barber, S.Iwata
compound source
Molecule: Photosystem Q(B) Protein
Chain: A, a
Synonym: 32 Kda Thylakoid Membrane Protein, Photosystem II D1;
 Organism_scientific: Thermosynechococcus Elongatus
Organism_taxid: 146786

Molecule: Photosystem II Core Light Harvesting Protein
Chain: B, b
Organism_scientific: Thermosynechococcus Elongatus
Organism_taxid: 146786

Molecule: Photosystem II Cp43 Protein
Chain: C, c
Organism_scientific: Thermosynechococcus Elongatus
Organism_taxid: 146786

Molecule: Photosystem II Reaction Center D2 Protein
Chain: D, d
Organism_scientific: Thermosynechococcus Elongatus
Organism_taxid: 146786

Molecule: Cytochrome B559 Alpha Subunit
Chain: E, e
Synonym: Psii Reaction Center Subunit V
Organism_scientific: Thermosynechococcus Elongatus
Organism_taxid: 146786

Molecule: Cytochrome B559 Beta Subunit
Chain: F, f
Synonym: Psii Reaction Center Subunit Vi
Organism_scientific: Thermosynechococcus Elongatus
Organism_taxid: 146786

Molecule: Photosystem II Psbh Protein
Chain: H, h
Organism_scientific: Thermosynechococcus Elongatus
Organism_taxid: 146786

Molecule: Photosystem II Reaction Center I Protein
Chain: I, I
Synonym: Psii 4.4 Kda Protein
Organism_scientific: Thermosynechococcus Elongatus
Organism_taxid: 146786

Molecule: Photosystem II Reaction Center J Protein
Chain: J, j
Organism_scientific: Thermosynechococcus Elongatus
Organism_taxid: 146786

Molecule: Photosystem II Reaction Center Protein K
Chain: K, k
Synonym: Psii-K
Organism_scientific: Thermosynechococcus Elongatus
Organism_taxid: 146786

Molecule: Photosystem II Reaction Center L Protein
Chain: L, l
Synonym: Psii 5 Kda Protein
Organism_scientific: Thermosynechococcus Elongatus
Organism_taxid: 146786

Molecule: Photosystem II Reaction Center M Protein
Chain: M, m
Synonym: Psii-M
Organism_scientific: Thermosynechococcus Elongatus
Organism_taxid: 146786

Molecule: Photosystem II Manganese-Stabilizing Polypeptide
Chain: O, o
Synonym: Msp
Organism_scientific: Thermosynechococcus Elongatus
Organism_taxid: 146786

Molecule: Photosystem II Psbt Protein
Chain: T, t
Organism_scientific: Thermosynechococcus Elongatus
Organism_taxid: 146786

Molecule: Photosystem II 12 Kda Extrinsic Protein
Chain: U, u
Synonym: Ps II Complex 12 Kda Extrinsic Protein, Psii-U
Organism_scientific: Thermosynechococcus Elongatus
Organism_taxid: 146786

Molecule: Cytochrome C-550
Chain: V, v
Synonym: C550, Low Potential Cytochrome C
Organism_scientific: Thermosynechococcus Elongatus
Organism_taxid: 146786

Molecule: Photosystem II Psbx Protein
Chain: X, x
Organism_scientific: Thermosynechococcus Elongatus
Organism_taxid: 146786

Molecule: Photosystem II Psbn Protein
Chain: N, n
Organism_scientific: Thermosynechococcus Elongatus
Organism_taxid: 146786

Molecule: Photosystem II Reaction Center Z Protein
Chain: Z, z
Synonym: Photosystem II Psbz Protein
Organism_scientific: Thermosynechococcus Elongatus
Organism_taxid: 146786
symmetry Space Group: P 21 21 21
R_factor 0.296 R_Free 0.342
crystal
cell
length a length b length c angle alpha angle beta angle gamma
134.992 228.849 309.940 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.50 Å
ligand BCR, BCT, CLA, FE, HEC, LMT, OEC, PHO, PL9 enzyme
note 1S5L (Molecule of the Month:pdb59)
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


    Z, z


    a, A


    c, C


    d, D


    j, J


    u, U


    v, V


    x, X


    Primary referenceArchitecture of the Photosynthetic Oxygen-Evolving Center., Ferreira KN, Iverson TM, Maghlaoui K, Barber J, Iwata S, Science 2004 Feb 5;. PMID:14764885
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (987 Kb) [Save to disk]
  • Biological Unit Coordinates (1s5l.pdb1.gz) 464 Kb
  • Biological Unit Coordinates (1s5l.pdb2.gz) 464 Kb
  • LPC: Ligand-Protein Contacts for 1S5L
  • CSU: Contacts of Structural Units for 1S5L
  • Likely Quarternary Molecular Structure file(s) for 1S5L
  • Structure Factors (4138 Kb)
  • Retrieve 1S5L in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1S5L from S2C, [Save to disk]
  • Re-refined 1s5l structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1S5L 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 1S5L
  • 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
  • 3D motif for 1S5L, from MSDmotif at EBI
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1s5l_u] [1s5l_k] [1s5l_T] [1s5l_n] [1s5l_J] [1s5l_v] [1s5l_Z] [1s5l_A] [1s5l_d] [1s5l_b] [1s5l_F] [1s5l_e] [1s5l_L] [1s5l_x] [1s5l_X] [1s5l_N] [1s5l_f] [1s5l_V] [1s5l_I] [1s5l_z] [1s5l_M] [1s5l_O] [1s5l_U] [1s5l_E] [1s5l_h] [1s5l_l] [1s5l_B] [1s5l_K] [1s5l_H] [1s5l_t] [1s5l_D] [1s5l_C] [1s5l_i] [1s5l_o] [1s5l_c] [1s5l_j] [1s5l] [1s5l_m] [1s5l_a]
  • SWISS-PROT database: [P0A386] [P0A444] [Q8CM25] [Q8DIP0] [Q8DIN9] [Q8DJ43] [Q8DJZ6] [P59087] [Q9F1K9] [Q8DIN8] [Q8DHA7] [P0A431] [Q8DIQ0] [Q9F1L5] [Q9F1R6] [Q8DHJ2] [Q8DIF8] [Q8DIQ1]
  • Domain organization of [CY550_THEEB] [PSBA1_THEEB] [PSBD_THEEB] [PSBE_THEEB] [PSBF_THEEB] [PSBH_THEEB] [PSBI_THEEB] [PSBJ_THEEB] [PSBK_THEEB] [PSBL_THEEB] [PSBM_THEEB] [PSBO_THEEB] [PSBT_THEEB] [PSBU_THEEB] [PSBX_THEEB] [PSBZ_THEEB] [Q8DIF8_THEEB] [Q8DIQ1_THEEB] by SWISSPFAM
    • Other resources with information on 1S5L
  • Community annotation for 1S5L at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
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