- PDB-2bpb: Sulfite dehydrogenase from Starkeya Novella -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 2bpb
Title
Sulfite dehydrogenase from Starkeya Novella
Components
SULFITE\:CYTOCHROME C OXIDOREDUCTASE SUBUNIT A
SULFITE\:CYTOCHROME C OXIDOREDUCTASE SUBUNIT B
Keywords
OXIDOREDUCTASE / SULFITE OXIDASE / MOLYBDOPTERIN / C-TYPE CYTOCHROME / HEME / ELECTRON TRANSPORT
Function / homology
Function and homology information
sulfite oxidase activity / sulfur compound metabolic process / molybdenum ion binding / molybdopterin cofactor binding / electron transfer activity / heme binding / metal ion binding Similarity search - Function
HEME C / (MOLYBDOPTERIN-S,S)-OXO-MOLYBDENUM / Sulfite:cytochrome c oxidoreductase subunit B / Sulfite:cytochrome c oxidoreductase subunit A Similarity search - Component
Biological species
STARKEYA NOVELLA (bacteria)
Method
X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.9 Å
Journal: J.Biol.Chem. / Year: 2005 Title: Molecular Basis of Intramolecular Electron Transfer in Sulfite-Oxidizing Enzymes is Revealed by High Resolution Structure of a Heterodimeric Complex of the Catalytic Molybdopterin Subunit and ...Title: Molecular Basis of Intramolecular Electron Transfer in Sulfite-Oxidizing Enzymes is Revealed by High Resolution Structure of a Heterodimeric Complex of the Catalytic Molybdopterin Subunit and a C-Type Cytochrome Subunit. Authors: Kappler, U. / Bailey, S.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: Crystallisation and Preliminary X-Ray Analysis of Sulfite Dehydrogenase from Starkeya Novella. Authors: Kappler, U. / Bailey, S.
History
Deposition
Apr 19, 2005
Deposition site: PDBE / Processing site: PDBE
Revision 1.0
Apr 28, 2005
Provider: repository / Type: Initial release
Revision 1.1
May 8, 2011
Group: Version format compliance
Revision 1.2
Jul 13, 2011
Group: Version format compliance
Remark 700
SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.
THE DIMER DESCRIBED HERE IS ACTUALLY A HETERO-DIMER, FORMEDFROM CHAINS A AND B. THE HETERO-DIMER IS KNOWN TO BE STABLEIN SOLUTION. FOR THE HETERO-ASSEMBLY DESCRIBED BY REMARK 350
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Components
#1: Protein
SULFITE\:CYTOCHROMECOXIDOREDUCTASESUBUNITA / SORA
Mass: 40194.719 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STARKEYA NOVELLA (bacteria) / Production host: RHODOBACTER CAPSULATUS (bacteria) / References: UniProt: Q9LA16
#2: Protein
SULFITE\:CYTOCHROMECOXIDOREDUCTASESUBUNITB / SORB
Mass: 8844.831 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STARKEYA NOVELLA (bacteria) / Production host: RHODOBACTER CAPSULATUS (bacteria) / References: UniProt: Q9LA15
Type: MARRESEARCH / Detector: CCD / Date: Nov 4, 2004
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.074 Å / Relative weight: 1
Reflection
Resolution: 1.9→36 Å / Num. obs: 40189 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.5
Reflection shell
Resolution: 1.9→2 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.8 / % possible all: 97.7
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Processing
Software
Name
Version
Classification
REFMAC
5.2.0005
refinement
MOSFLM
datareduction
SCALA
datascaling
Refinement
Method to determine structure: OTHER / Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.922 / SU B: 2.977 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.21
2047
5.1 %
RANDOM
Rwork
0.166
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obs
0.168
38033
97.6 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK