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Yorodumi- PDB-2a9d: Crystal structure of recombinant chicken sulfite oxidase with Arg... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2a9d | ||||||
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Title | Crystal structure of recombinant chicken sulfite oxidase with Arg at residue 161 | ||||||
Components | Sulfite Oxidase | ||||||
Keywords | OXIDOREDUCTASE / sulfite oxidase / Molybdopterin / Molybdenum | ||||||
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: 1.701 Å | ||||||
Authors | Karakas, E. / Wilson, H.L. / Graf, T.N. / Xiang, S. / Jaramillo-Busquets, S. / Rajagopalan, K.V. / Kisker, C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Structural insights into sulfite oxidase deficiency Authors: Karakas, E. / Wilson, H.L. / Graf, T.N. / Xiang, S. / Jaramillo-Busquets, S. / Rajagopalan, K.V. / Kisker, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2a9d.cif.gz | 176.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2a9d.ent.gz | 134.7 KB | Display | PDB format |
PDBx/mmJSON format | 2a9d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a9/2a9d ftp://data.pdbj.org/pub/pdb/validation_reports/a9/2a9d | HTTPS FTP |
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-Related structure data
Related structure data | 2a99C 2a9aC 2a9bC 2a9cC 1soxS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 4
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Details | The asymmetric unit contains a dimer which is the functional unit |
-Components
#1: Protein | Mass: 40733.965 Da / Num. of mol.: 2 Fragment: Catalytic core domain and C terminal dimerization domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) Description: The gene is chemically synthesized based on the protein sequence of sulfite oxidase from Gallus gallus Cellular location: Mitochondrial Intermembrane SpaceMitochondrion Gene: SUOX / Organ: Liver / Organelle: Mitochondrion / Plasmid: pTrc99A / Production host: Escherichia coli (E. coli) / Strain (production host): TP1000 / References: UniProt: P07850, sulfite oxidase #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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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: 2.37 Å3/Da / Density % sol: 47.78 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 8000, MES, Magnesium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.25 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 24, 2004 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.25 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→30 Å / Num. obs: 77687 / % possible obs: 95.1 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.071 / Χ2: 1.535 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 1SOX Resolution: 1.701→30 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.354 / SU ML: 0.064 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.098 / 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: 20.761 Å2
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Refinement step | Cycle: LAST / Resolution: 1.701→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 5341 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.701→1.745 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 | Refine-ID: X-RAY DIFFRACTION / Selection: ALL
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