+Open data
-Basic information
Entry | Database: PDB / ID: 2c9x | ||||||
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Title | Sulfite dehydrogenase from Starkeya Novella Y236F mutant | ||||||
Components | (SULFITE\:CYTOCHROME C OXIDOREDUCTASE SUBUNIT ...) x 2 | ||||||
Keywords | OXIDOREDUCTASE / SULFITE OXIDASE / MOLYBDOPTERIN / C-TYPE CYTOCHROME / HEME / MUTANT | ||||||
Function / homology | Function and homology information molybdenum ion binding / electron transfer activity / oxidoreductase activity / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | THIOBACILLUS NOVELLUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Bailey, S. / Kappler, U. / Feng, C. / Honeychurch, M.J. / Bernhardt, P. / Tollin, G. / Enemark, J. | ||||||
Citation | Journal: Biochemistry / Year: 2006 Title: Kinetic and Structural Evidence for the Importance of Tyr236 for the Integrity of the Mo Active Site in a Bacterial Sulfite Dehydrogenase. Authors: Kappler, U. / Bailey, S. / Feng, C. / Honeychurch, M.J. / Hanson, G.R. / Bernhardt, P. / Tollin, G. / Enemark, J. #1: Journal: J.Biol.Chem. / Year: 2005 Title: Molecular Basis of Intramolecular Electron Transfer in Sulfite-Oxidising 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-Oxidising 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. | ||||||
History |
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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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2c9x.cif.gz | 114.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c9x.ent.gz | 85.4 KB | Display | PDB format |
PDBx/mmJSON format | 2c9x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c9/2c9x ftp://data.pdbj.org/pub/pdb/validation_reports/c9/2c9x | HTTPS FTP |
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-Related structure data
Related structure data | 2blfS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-SULFITE\:CYTOCHROME C OXIDOREDUCTASE SUBUNIT ... , 2 types, 2 molecules AB
#1: Protein | Mass: 40178.719 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) THIOBACILLUS NOVELLUS (bacteria) / Production host: RHODOBACTER CAPSULATUS (bacteria) / References: UniProt: Q9LA16 |
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#2: Protein | Mass: 8844.831 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) THIOBACILLUS NOVELLUS (bacteria) / Production host: RHODOBACTER CAPSULATUS (bacteria) / References: UniProt: Q9LA15 |
-Non-polymers , 4 types, 424 molecules
#3: Chemical | ChemComp-MSS / ( |
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#4: Chemical | ChemComp-SO4 / |
#5: Chemical | ChemComp-HEC / |
#6: Water | ChemComp-HOH / |
-Details
Compound details | ENGINEEREDSequence details | THE TRANSLATED SEQUENCES FOR CHAINS A AND B INCLUDE SIGNAL PEPTIDES WHICH ARE NOT PART OF THE ...THE TRANSLATED | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 46 % |
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Crystal grow | pH: 7.4 Details: 0.1M HEPES PH 7.4, 2.2M AMMONIUM SULFATE, 2% PEG200 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.98 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 5, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 46488 / % possible obs: 96.8 % / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 4 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.2 / % possible all: 82.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BLF Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.387 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.31 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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