3P4P Oxidoreductase date Oct 06, 2010
title Crystal Structure Of Menaquinol:Fumarate Oxidoreductase In C With Fumarate
authors T.M.Tomasiak, T.L.Archuleta, J.Andr Ll, C.Luna-Ch Vez, T.A.Davis M.Sarwar, A.J.Ham, W.H.Mcdonald, V.Yankowskaya, H.A.Stern, J.N.J E.Maklashina, G.Cecchini, T.M.Iverson
compound source
Molecule: Fumarate Reductase Flavoprotein Subunit
Chain: A, M
Fragment: Unp Residues 1-577
Ec: 1.3.99.1
Engineered: Yes
Organism_scientific: Escherichia Coli 042
Organism_taxid: 216592
Strain: 042 Eaec
Gene: Frda, Ec042_4630
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Fumarate Reductase Iron-Sulfur Protein
Chain: B, N
Ec: 1.3.99.1
Engineered: Yes

Organism_scientific: Escherichia Coli 536
Organism_taxid: 362663
Strain: 536 Upec
Gene: Ecp_4399
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Fumarate Reductase Subunit C
Chain: C, O
Engineered: Yes

Organism_scientific: Escherichia Coli Dh1
Organism_taxid: 536056
Strain: Atcc 33849 Dsm 4235 Ncib 12045 K12 Dh1
Gene: Frdc, Ecdh1_3838
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Fumarate Reductase Subunit D
Chain: D, P
Engineered: Yes

Organism_scientific: Escherichia Coli Dh1
Organism_taxid: 536056
Strain: Atcc 33849 Dsm 4235 Ncib 12045 K12 Dh1
Gene: Frdd, Ecdh1_3839
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.249 R_Free 0.272
crystal
cell
length a length b length c angle alpha angle beta angle gamma
96.317 137.633 270.684 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand F3S, FAD, FES, FUM, SF4 enzyme Oxidoreductase E.C.1.3.99.1 BRENDA
Gene EC042 ; ECDH1 ; ECDH1 ; ECP
Gene
Ontology
ChainFunctionProcessComponent
A, M


D, P


N, B
  • electron transfer activity


  • O, C


    Primary referenceGeometric restraint drives on- and off-pathway catalysis by the Escherichia coli menaquinol:fumarate reductase., Tomasiak TM, Archuleta TL, Andrell J, Lunz-Chavez C, Davis TA, Sarwar M, Ham AJ, McDonald WH, Yankovskaya V, Stern HA, Johnston JN, McLashina E, Cecchini G, Iverson TM, J Biol Chem. 2010 Nov 23. PMID:21098488
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (705 Kb) [Save to disk]
  • Biological Unit Coordinates (3p4p.pdb1.gz) 342 Kb
  • Biological Unit Coordinates (3p4p.pdb2.gz) 360 Kb
  • LPC: Ligand-Protein Contacts for 3P4P
  • CSU: Contacts of Structural Units for 3P4P
  • Structure Factors (660 Kb)
  • Retrieve 3P4P in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3P4P from S2C, [Save to disk]
  • Re-refined 3p4p structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3P4P 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 3P4P
  • 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 3P4P, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3p4p_B] [3p4p_P] [3p4p_A] [3p4p_O] [3p4p_M] [3p4p] [3p4p_N] [3p4p_D] [3p4p_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3P4P
  • Community annotation for 3P4P at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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