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Yorodumi- PDB-8hdn: Brucella melitensis 7-alpha-Hydroxysteroid Dehydrogenase mutant: ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8hdn | |||||||||
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Title | Brucella melitensis 7-alpha-Hydroxysteroid Dehydrogenase mutant: 1-53 truncation-I258M/K262T | |||||||||
Components | 7-alpha-hydroxysteroid dehydrogenase | |||||||||
Keywords | OXIDOREDUCTASE / SDR family / hydroxysteroid dehydrogenase | |||||||||
Function / homology | Function and homology information 7alpha-hydroxysteroid dehydrogenase / cholate 7-alpha-dehydrogenase activity / nucleotide binding Similarity search - Function | |||||||||
Biological species | Brucella melitensis biotype 1 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | |||||||||
Authors | Liu, Z.Y. / Zhang, R.Z. | |||||||||
Funding support | China, 2items
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Citation | Journal: To Be Published Title: Structure of 7-alpha-hydroxysteroid dehydrogenase Authors: Liu, Z.Y. / Zhang, R.Z. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hdn.cif.gz | 199.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hdn.ent.gz | 156.6 KB | Display | PDB format |
PDBx/mmJSON format | 8hdn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8hdn_validation.pdf.gz | 443.1 KB | Display | wwPDB validaton report |
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Full document | 8hdn_full_validation.pdf.gz | 444.9 KB | Display | |
Data in XML | 8hdn_validation.xml.gz | 41.6 KB | Display | |
Data in CIF | 8hdn_validation.cif.gz | 61.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hd/8hdn ftp://data.pdbj.org/pub/pdb/validation_reports/hd/8hdn | HTTPS FTP |
-Related structure data
Related structure data | 8hdeC 8hdiC 8hs4C 8hs5C 8hs6C 8hs9C 8hsaC 1fmcS 3gafS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 25872.635 Da / Num. of mol.: 4 / Fragment: 1-53 truncation Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brucella melitensis biotype 1 (strain 16M / ATCC 23456 / NCTC 10094) (bacteria) Gene: BMEI0406 / Production host: Escherichia coli (E. coli) References: UniProt: Q8YIN7, 7alpha-hydroxysteroid dehydrogenase #2: 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: 2.61 Å3/Da / Density % sol: 52.81 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1M MIB, 10% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.987 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 12, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→44.13 Å / Num. obs: 113642 / % possible obs: 99.9 % / Redundancy: 9.9 % / Biso Wilson estimate: 12.68 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.044 / Rrim(I) all: 0.139 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.7→1.763 Å / Rmerge(I) obs: 0.743 / Mean I/σ(I) obs: 10.9 / Num. unique obs: 11259 / CC1/2: 0.865 / Rpim(I) all: 0.334 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3GAF, 1FMC Resolution: 1.7→33.96 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 20.44 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→33.96 Å
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Refine LS restraints | Type: f_bond_d / Dev ideal: 0.006 / Number: 7141 | ||||||||||||||||||||
LS refinement shell | Resolution: 1.7→1.79 Å
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