3D38 Photosynthesis date May 09, 2008
title Crystal Structure Of New Trigonal Form Of Photosynthetic Rea Center From Blastochloris Viridis. Crystals Grown In Microf Detergent Capture.
authors L.Li, S.H.M.Nachtergaele, A.M.Seddon, V.Tereshko, N.Ponomarenko, R.F.Ismagilov, Accelerated Technologies Center For Gene To 3 Structure (Atcg3d)
compound source
Molecule: Photosynthetic Reaction Center Cytochrome C Subun
Chain: C
Synonym: Cytochrome C558c559
Organism_scientific: Blastochloris Viridis
Organism_taxid: 1079
Atcc: 19567

Molecule: Reaction Center Protein H Chain
Chain: H
Synonym: Photosynthetic Reaction Center H Subunit

Organism_scientific: Blastochloris Viridis
Organism_taxid: 1079
Atcc: 19567

Molecule: Reaction Center Protein L Chain
Chain: L
Synonym: Photosynthetic Reaction Center L Subunit

Organism_scientific: Blastochloris Viridis
Organism_taxid: 1079
Atcc: 19567

Molecule: Reaction Center Protein M Chain
Chain: M
Synonym: Photosynthetic Reaction Center M Subunit

Organism_scientific: Blastochloris Viridis
Organism_taxid: 1079
Atcc: 19567
symmetry Space Group: P 31 2 1
R_factor 0.192 R_Free 0.224
crystal
cell
length a length b length c angle alpha angle beta angle gamma
241.171 241.171 113.391 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.21 Å
ligand BCB, BPB, FE2, FME, HEC, HTO, LDA, MQ9, NS5, SO4, UQ1 enzyme
Gene
Ontology
ChainFunctionProcessComponent
C
  • electron transfer activity


  • H
  • electron transporter, transf...


  • L


    M


    Primary referenceSimple host-guest chemistry to modulate the process of concentration and crystallization of membrane proteins by detergent capture in a microfluidic device., Li L, Nachtergaele S, Seddon AM, Tereshko V, Ponomarenko N, Ismagilov RF, J Am Chem Soc. 2008 Oct 29;130(43):14324-8. Epub 2008 Oct 3. PMID:18831551
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (218 Kb) [Save to disk]
  • Biological Unit Coordinates (3d38.pdb1.gz) 205 Kb
  • LPC: Ligand-Protein Contacts for 3D38
  • CSU: Contacts of Structural Units for 3D38
  • Likely Quarternary Molecular Structure file(s) for 3D38
  • Structure Factors (992 Kb)
  • Retrieve 3D38 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3D38 from S2C, [Save to disk]
  • Re-refined 3d38 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3D38 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 3D38
  • 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 3D38, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3d38_C] [3d38_L] [3d38_M] [3d38] [3d38_H]
  • SWISS-PROT database: [P07173] [P06008] [P06009] [P06010]
  • Domain organization of [CYCR_RHOVI] [RCEH_RHOVI] [RCEL_RHOVI] [RCEM_RHOVI] by SWISSPFAM
  • Other resources with information on 3D38
  • Community annotation for 3D38 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
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