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Yorodumi- PDB-3hbg: Structure of recombinant Chicken Liver Sulfite Oxidase mutant C185S -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hbg | ||||||
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Title | Structure of recombinant Chicken Liver Sulfite Oxidase mutant C185S | ||||||
Components | Sulfite Oxidase mutant C185S | ||||||
Keywords | OXIDOREDUCTASE / sulfite oxidase / molybdenum / molybdopterin / oxotransferase | ||||||
Function / homology | Function and homology information sulfite oxidase / sulfite oxidase activity / sulfur compound metabolic process / molybdenum ion binding / molybdopterin cofactor binding / mitochondrial intermembrane space / heme binding / mitochondrion Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Qiu, J.A. | ||||||
Citation | Journal: Biochemistry / Year: 2010 Title: The structures of the C185S and C185A mutants of sulfite oxidase reveal rearrangement of the active site. Authors: Qiu, J.A. / Wilson, H.L. / Pushie, M.J. / Kisker, C. / George, G.N. / Rajagopalan, K.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hbg.cif.gz | 90 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hbg.ent.gz | 65 KB | Display | PDB format |
PDBx/mmJSON format | 3hbg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3hbg_validation.pdf.gz | 822.7 KB | Display | wwPDB validaton report |
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Full document | 3hbg_full_validation.pdf.gz | 825.1 KB | Display | |
Data in XML | 3hbg_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 3hbg_validation.cif.gz | 23.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hb/3hbg ftp://data.pdbj.org/pub/pdb/validation_reports/hb/3hbg | HTTPS FTP |
-Related structure data
Related structure data | 3hbpC 3hbqC 2a99S S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 50985.125 Da / Num. of mol.: 1 / Fragment: rCSO C185S residues 94 to 466 / Mutation: C185S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Plasmid: pTRC99a / Production host: Escherichia coli (E. coli) / Strain (production host): TP1000 / References: UniProt: P07850*PLUS |
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#2: Chemical | ChemComp-MTE / |
#3: Chemical | ChemComp-MOM / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.39 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 15% (v/v) MPD, 2% PEG 4000 (w/v), and 100 mM Sodium Acetate pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 22, 2007 |
Radiation | Monochromator: Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→27.38 Å / Num. obs: 43889 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Rsym value: 0.056 / Net I/σ(I): 50.5 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 4.6 / Rsym value: 0.263 / % possible all: 85.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: recombinant Chicken liver sulfite oxidase 2A99 Resolution: 1.9→27.38 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.96 / SU B: 4.388 / SU ML: 0.064 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.101 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.684 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→27.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.899→1.949 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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