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Yorodumi- PDB-4hvn: Crystal structure of hypothetical protein with ketosteroid isomer... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hvn | ||||||
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Title | Crystal structure of hypothetical protein with ketosteroid isomerase-like protein fold from Catenulispora acidiphila DSM 44928 in complex with Trimethylamine. | ||||||
Components | hypothetical protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-Biology / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | 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 / N,N-dimethylmethanamine / SnoaL-like domain-containing protein Function and homology information | ||||||
Biological species | Catenulispora acidiphila (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 | 4hvn.cif.gz | 113.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hvn.ent.gz | 87.6 KB | Display | PDB format |
PDBx/mmJSON format | 4hvn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4hvn_validation.pdf.gz | 445.8 KB | Display | wwPDB validaton report |
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Full document | 4hvn_full_validation.pdf.gz | 446.7 KB | Display | |
Data in XML | 4hvn_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | 4hvn_validation.cif.gz | 16.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hv/4hvn ftp://data.pdbj.org/pub/pdb/validation_reports/hv/4hvn | HTTPS FTP |
-Related structure data
Related structure data | 4h3uSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-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 / NRRL B-24433 / NBRC 102108 / JCM 14897 / Gene: Caci_0382 / Plasmid: pMCSG57 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: C7PVH9 #2: Chemical | ChemComp-KEN / #3: 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: 2.01 Å3/Da / Density % sol: 38.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1 M Bis-Tris, 25% PEG3350, pH 5.5, 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: 0.97856 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 25, 2012 / Details: MIRROR |
Radiation | Monochromator: SI-111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→30 Å / Num. all: 20052 / Num. obs: 20052 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 36.3 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 20.9 |
Reflection shell | Resolution: 1.95→1.98 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 964 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4H3U Resolution: 1.95→29.78 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / SU B: 8.093 / SU ML: 0.11 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.142 / 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: 38.523 Å2
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Refine analyze | Luzzati coordinate error obs: 0.23 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→29.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.947→1.998 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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