3BVD	Oxidoreductase	date	Jan 07, 2008
title	Structure Of Surface-Engineered Cytochrome Ba3 Oxidase From Thermophilus Under Xenon Pressure, 100psi 5min
authors	V.M.Luna, Y.Chen, J.A.Fee, C.D.Stout
compound		source
Molecule: Cytochrome C Oxidase Subunit 1 Chain: A Synonym: Cytochrome C Oxidase Polypeptide I, Cytochrome C B Subunit I, Cytochrome Cba3 Subunit 1; Ec: 1.9.3.1 Engineered: Yes Mutation: Yes		Organism_scientific: Thermus Thermophilus Strain: Hb8 Atcc: 27634 Gene: Cbaa Expression_system: Thermus Thermophilus Expression_system_strain: Hb8 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pmk18
Molecule: Cytochrome C Oxidase Subunit 2 Chain: B Synonym: Cytochrome C Oxidase Polypeptide II, Cytochrome C Subunit II, Cytochrome Cba3 Subunit 2; Ec: 1.9.3.1 Engineered: Yes Mutation: Yes		Organism_scientific: Thermus Thermophilus Strain: Hb8 Atcc: 27634 Gene: Cbab, Ctac Expression_system: Thermus Thermophilus Expression_system_strain: Hb8 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pmk18
Molecule: Cytochrome C Oxidase Polypeptide 2a Chain: C Synonym: Cytochrome C Oxidase Polypeptide Iia, Cytochrome C Subunit Iia, Cytochrome Cba3 Subunit 2a; Ec: 1.9.3.1 Engineered: Yes		Organism_scientific: Thermus Thermophilus Strain: Hb8 Atcc: 27634 Gene: Cbad Expression_system: Thermus Thermophilus Expression_system_strain: Hb8 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pmk18
symmetry	Space Group: P 41 21 2	R_factor 0.292 R_Free 0.336
crystal cell	length a length b length c angle alpha angle beta angle gamma 119.726 119.726 153.535 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	3.37 Å
ligand	CU, CUA, HAS, HEM, XE	enzyme	Oxidoreductase E.C.1.9.3.1 BRENDA
Gene Ontology	Chain Function Process Component A cytochrome-c oxidase activit... B cytochrome-c oxidase activit... C
Primary reference	Crystallographic Studies of Xe and Kr Binding within the Large Internal Cavity of Cytochrome ba3 from Thermus thermophilus: Structural Analysis and Role of Oxygen Transport Channels in the Heme-Cu Oxidases(,)., Luna VM, Chen Y, Fee JA, Stout CD, Biochemistry. 2008 Apr 22;47(16):4657-65. Epub 2008 Apr 1. PMID:18376849

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (109 Kb) [Save to disk] Biological Unit Coordinates (3bvd.pdb1.gz) 103 Kb LPC: Ligand-Protein Contacts for 3BVD CSU: Contacts of Structural Units for 3BVD Likely Quarternary Molecular Structure file(s) for 3BVD Structure Factors (252 Kb) Retrieve 3BVD in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3BVD from S2C, [Save to disk] Re-refined 3bvd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3BVD 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 3BVD

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 3BVD, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3bvd_C] [3bvd_A] [3bvd] [3bvd_B] SWISS-PROT database: [Q5SJ79] [Q5SJ80] [P82543] Belongs to the proton-translocating cytochrome oxidase (cox) superfamily according to TCDB. Domain organization of [COX1_THET8] [COX2_THET8] [COXA_THET8] by SWISSPFAM

Other resources with information on 3BVD

Community annotation for 3BVD at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

You may enter another PDB ID code

Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]

---

OCA© by Jaime Prilusky, 1996-2014,2022 Bioinformatics Unit Weizmann Institute of Science

---