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Yorodumi- PDB-4qm9: Crystal Structure of a Putative Cysteine Dioxygenase From Bacillu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qm9 | ||||||
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Title | Crystal Structure of a Putative Cysteine Dioxygenase From Bacillus subtilis with Cys-bound | ||||||
Components | Cysteine dioxygenase | ||||||
Keywords | OXIDOREDUCTASE / Cupin fold / catalyzes oxidation of cysteine to cysteine sulfinate | ||||||
Function / homology | Function and homology information cysteine dioxygenase / cysteine dioxygenase activity / L-cysteine catabolic process / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / ferrous iron binding Similarity search - Function | ||||||
Biological species | Bacillus subtilis subsp. subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Hartman, S.H. / Driggers, C.M. / Karplus, P.A. | ||||||
Citation | Journal: Protein Sci. / Year: 2015 Title: Structures of Arg- and Gln-type bacterial cysteine dioxygenase homologs. Authors: Driggers, C.M. / Hartman, S.J. / Karplus, P.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qm9.cif.gz | 137.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qm9.ent.gz | 106.9 KB | Display | PDB format |
PDBx/mmJSON format | 4qm9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qm/4qm9 ftp://data.pdbj.org/pub/pdb/validation_reports/qm/4qm9 | HTTPS FTP |
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-Related structure data
Related structure data | 4qm8C 4qmaC 3eqeS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 19614.113 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria) Strain: 168 / Gene: BSU31140, cdoA, Cysteine Dioxygenase, yubC / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21-DE3 / References: UniProt: O32085, cysteine dioxygenase #2: Chemical | #3: Chemical | #4: 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: 2.73 Å3/Da / Density % sol: 54.91 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: Purified enzyme was concentrated to 10 mg/mL and 4 uL was mixed with 4 uL of a reservoir containing 18% (w/v) PEG 4000, 0.1 M potassium acetate, 0.05 M MES, pH 6.0, VAPOR DIFFUSION, HANGING ...Details: Purified enzyme was concentrated to 10 mg/mL and 4 uL was mixed with 4 uL of a reservoir containing 18% (w/v) PEG 4000, 0.1 M potassium acetate, 0.05 M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.976 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 12, 2013 |
Radiation | Monochromator: Si(220) Asymmetric cut single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 20271 / Num. obs: 20271 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 23.4 % / Rmerge(I) obs: 0.186 / Rsym value: 0.038 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 13.7 % / Rmerge(I) obs: 2.892 / Mean I/σ(I) obs: 1 / Num. unique all: 1939 / Rsym value: 0.767 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3eqe Resolution: 2.3→46.66 Å / SU ML: 0.41 / σ(F): 1.33 / Phase error: 29.51 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→46.66 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | S33: -0.0256 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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