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Yorodumi- PDB-4h3u: Crystal structure of hypothetical protein with ketosteroid isomer... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4h3u | ||||||
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Title | Crystal structure of hypothetical protein with ketosteroid isomerase-like protein fold from Catenulispora acidiphila DSM 44928 | ||||||
Components | hypothetical protein | ||||||
Keywords | Structural Genomics / Unknown Function / PSI-Biology / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information SnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Catenulispora acidiphila (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.15 Å | ||||||
Authors | Filippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Jedrzejczak, R. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: J.Struct.Funct.Genom. / Year: 2014 Title: Structural characterization of a hypothetical protein: a potential agent involved in trimethylamine metabolism in Catenulispora acidiphila. Authors: Filippova, E.V. / Luan, C.H. / Dunne, S.F. / Kiryukhina, O. / Minasov, G. / Shuvalova, L. / Anderson, W.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4h3u.cif.gz | 134.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4h3u.ent.gz | 111.2 KB | Display | PDB format |
PDBx/mmJSON format | 4h3u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h3/4h3u ftp://data.pdbj.org/pub/pdb/validation_reports/h3/4h3u | HTTPS FTP |
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-Related 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: 17246.256 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Catenulispora acidiphila (bacteria) / Strain: DSM 44928 / Gene: Caci_0382 / Plasmid: pMCSG73 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: C7PVH9 #2: Chemical | ChemComp-CD / #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-ACT / #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: 2.29 Å3/Da / Density % sol: 46.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.05 M Cadmium Sulfate, 0.1 M Hepes, 0.5 M Sodium acetate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 13, 2012 / Details: MIRROR |
Radiation | Monochromator: SI-111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→50 Å / Num. all: 212580 / Num. obs: 212580 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 14.6 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 34.7 |
Reflection shell | Resolution: 1.15→1.17 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.8 / Num. unique all: 10416 / % possible all: 95.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.15→29.94 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.838 / SU ML: 0.018 / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.027 / ESU R Free: 0.026 / 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: 14.577 Å2
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Refine analyze | Luzzati coordinate error obs: 0.1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.15→29.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.15→1.18 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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