4L6V Electron Transport date Jun 13, 2013
title Crystal Structure Of A Virus Like Photosystem I From The Cyanobacterium Synechocystis Pcc 6803
authors Y.Mazor, D.Nataf, H.Toporik, N.Nelson
compound source
Molecule: Photosystem I P700 Chlorophyll A Apoprotein A1
Chain: A, a, 1
Synonym: Psaa
Ec: 1.97.1.12
Engineered: Yes
Organism_scientific: Synechocystis Sp. Pcc 6803
Organism_taxid: 1148
Gene: Psaa, Best7613_2234, Myo_18690
Expression_system: Synechocystis Sp. Pcc 6803
Expression_system_taxid: 1148

Molecule: Photosystem I P700 Chlorophyll A Apoprotein A2
Chain: B, b, 2
Synonym: Psab
Ec: 1.97.1.12
Engineered: Yes

Organism_scientific: Synechocystis Sp. Pcc 6803
Organism_taxid: 1148
Gene: Psab, Best7613_2235, Myo_18700
Expression_system: Synechocystis Sp. Pcc 6803
Expression_system_taxid: 1148

Molecule: Photosystem I Iron-Sulfur Center
Chain: C, c, 3
Synonym: 9 Kda Polypeptide, Psi-C, Photosystem I Subunit Vi
Ec: 1.97.1.12
Engineered: Yes

Organism_scientific: Synechocystis Sp. Pcc 6803
Organism_taxid: 1148
Gene: Psac, Best7613_5694, Myo_120930
Expression_system: Synechocystis Sp. Pcc 6803
Expression_system_taxid: 1148

Molecule: Photosystem I Subunit II
Chain: D, d, 4
Ec: 1.97.1.12
Engineered: Yes

Organism_scientific: Synechocystis Sp. Pcc 6803
Organism_taxid: 1148
Gene: Psae, Best7613_5968, Myo_118260
Expression_system: Synechocystis Sp. Pcc 6803
Expression_system_taxid: 1148

Molecule: Photosystem I Reaction Center Subunit Iv
Chain: E, e, 5
Ec: 1.97.1.12
Engineered: Yes

Organism_scientific: Synechocystis Sp. Pcc 6803
Organism_taxid: 1148
Gene: Psaf, Best7613_2928
Expression_system: Synechocystis Sp. Pcc 6803
Expression_system_taxid: 1148

Molecule: Fusion Protein Of Photosystem I Subunit III And S
Chain: F, f, 6
Synonym: Psi Subunit V, Psi-L
Ec: 1.97.1.12
Engineered: Yes

Organism_scientific: Synechocystis Sp. Pcc 6803, Bacillus S Best7613;
Organism_taxid: 1148, 1204343
Gene: Psal, Best7613_4425, Myo_131030, Psaf,Best7613_2928
Expression_system: Synechocystis Sp. Pcc 6803
Expression_system_taxid: 1148

Molecule: Photosystem I Reaction Center Subunit Xi
Chain: L, l, 8
Synonym: Psi-M
Ec: 1.97.1.12
Engineered: Yes

Organism_scientific: Synechocystis Sp. Pcc 6803
Organism_taxid: 1148
Gene: Psbm, Psam, Best7613_1787, Myo_14340
Expression_system: Synechocystis Sp. Pcc 6803
Expression_system_taxid: 1148

Molecule: Photosystem I Reaction Center Subunit Xii
Chain: M, m, 7
Ec: 1.97.1.12
Engineered: Yes

Organism_scientific: Synechocystis Sp. Pcc 6803
Organism_taxid: 1148
Gene: Psaf, Best7613_2928
Expression_system: Synechocystis Sp. Pcc 6803
Expression_system_taxid: 1148

Molecule: Photosystem I Subunit III
Chain: I, 9, I
Ec: 1.97.1.12
Engineered: Yes

Organism_scientific: Synechocystis Sp. Pcc 6803
Organism_taxid: 1148
Gene: Psai, Best7613_4424, Myo_131040
Expression_system: Synechocystis Sp. Pcc 6803
Expression_system_taxid: 1148

Molecule: Photosystem I Reaction Center Subunit Viii
Chain: K, k, 0
Ec: 1.97.1.12
Engineered: Yes

Organism_scientific: Synechocystis Sp. Pcc 6803
Organism_taxid: 1148
Gene: Psad, Best7613_1459, Myo_11100
Expression_system: Synechocystis Sp. Pcc 6803
Expression_system_taxid: 1148
symmetry Space Group: P 1 21 1
R_factor 0.253 R_Free 0.297
crystal
cell
length a length b length c angle alpha angle beta angle gamma
214.619 133.680 219.846 90.00 111.14 90.00
method X-Ray Diffractionresolution 3.80 Å
ligand BCR, CLA, LHG, LMG, PQN, SF4 enzyme Oxidoreductase E.C.1.97.1.12 BRENDA
subcellular loc. Membrane localization by OPM: Thylakoid membrane
thylakoid space side
stroma side
Gene BEST7613 ; BEST7613 ; BEST7613 ; BEST7613 ; BEST7613 ; BEST7613 ; BEST7613 ; BEST7613 ; BEST7613 ; BEST7613 ; MYO ; MYO ; MYO ; MYO ; MYO ; MYO ; MYO ; MYO ; MYO
Gene
Ontology
ChainFunctionProcessComponent
1, A


2, B


4, D


7, M


9, I


C, 3


E, 5


F, 6


K, 0


L, 8


a


b


c


d


e


k, f, i, m


l


Primary referenceCrystal structures of virus-like photosystem I complexes from the mesophilic cyanobacterium Synechocystis PCC 6803., Mazor Y, Nataf D, Toporik H, Nelson N, Elife. 2013 Jan 1;3:e01496. doi: 10.7554/eLife.01496. PMID:24473073
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (3130 Kb) [Save to disk]
  • Biological Unit Coordinates (4l6v.pdb1.gz) 1002 Kb
  • Biological Unit Coordinates (4l6v.pdb2.gz) 1022 Kb
  • Biological Unit Coordinates (4l6v.pdb3.gz) 1021 Kb
  • LPC: Ligand-Protein Contacts for 4L6V
  • CSU: Contacts of Structural Units for 4L6V
  • Structure Factors (2444 Kb)
  • Retrieve 4L6V in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4L6V from S2C, [Save to disk]
  • Re-refined 4l6v structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4L6V 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 4L6V
  • 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
  • 3D motif for 4L6V, from MSDmotif at EBI
  • Fold representative 4l6v from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4l6v] [4l6v_7] [4l6v_M] [4l6v_4] [4l6v_A] [4l6v_0] [4l6v_C] [4l6v_B] [4l6v_a] [4l6v_m] [4l6v_e] [4l6v_5] [4l6v_c] [4l6v_1] [4l6v_K] [4l6v_b] [4l6v_f] [4l6v_d] [4l6v_k] [4l6v_E] [4l6v_2] [4l6v_i] [4l6v_L] [4l6v_I] [4l6v_l] [4l6v_8] [4l6v_3] [4l6v_F] [4l6v_9] [4l6v_D] [4l6v_6]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4L6V
  • Community annotation for 4L6V at PDBWiki (http://pdbwiki.org)

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