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Yorodumi- PDB-8hdi: Brucella melitensis 7-alpha-Hydroxysteroid Dehydrogenase mutant: ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8hdi | |||||||||
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Title | Brucella melitensis 7-alpha-Hydroxysteroid Dehydrogenase mutant: 1-53 truncation/K262T | |||||||||
Components | 7-alpha-hydroxysteroid dehydrogenase | |||||||||
Keywords | OXIDOREDUCTASE / SDR family / hydroxysteroid dehydrogenase | |||||||||
Function / homology | 7alpha-hydroxysteroid dehydrogenase / cholate 7-alpha-dehydrogenase activity / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily / 7-alpha-hydroxysteroid dehydrogenase Function and homology information | |||||||||
Biological species | Brucella melitensis biotype 1 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 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 | 8hdi.cif.gz | 195.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hdi.ent.gz | 153.7 KB | Display | PDB format |
PDBx/mmJSON format | 8hdi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hd/8hdi ftp://data.pdbj.org/pub/pdb/validation_reports/hd/8hdi | HTTPS FTP |
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-Related structure data
Related structure data | 8hdeC 8hdnC 8hs4C 8hs5C 8hs6C 8hs9C 8hsaC 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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Unit cell |
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-Components
#1: Protein | Mass: 25854.598 Da / Num. of mol.: 4 / Fragment: 1-53 truncation / Mutation: K262T Source method: isolated from a genetically manipulated source Details: Sequence reference for WP_014489477 is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id Q8YIN7. Source: (gene. exp.) Brucella melitensis biotype 1 (strain 16M / ATCC 23456 / NCTC 10094) (bacteria) Gene: BMEI0406 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q8YIN7, 7alpha-hydroxysteroid dehydrogenase #2: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.58 Å3/Da / Density % sol: 52.39 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 0.1M MIB, 10% PEG3350 / PH range: 4.0-8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 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: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→43.18 Å / Num. obs: 73068 / % possible obs: 99.9 % / Redundancy: 9.9 % / Biso Wilson estimate: 23.48 Å2 / CC1/2: 0.996 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.99→2.07 Å / Redundancy: 10.1 % / Mean I/σ(I) obs: 6.6 / Num. unique obs: 73517 / CC1/2: 0.972 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→42.06 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 20.82 / 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: 1.99→42.06 Å
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Refine LS restraints |
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LS refinement shell |
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