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Yorodumi- PDB-8hsa: Brucella melitensis 7-alpha-Hydroxysteroid Dehydrogenase mutant: ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8hsa | |||||||||
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Title | Brucella melitensis 7-alpha-Hydroxysteroid Dehydrogenase mutant: 1-53 truncation/M196I/I258M/K262T-NAD+ | |||||||||
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 / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 7-alpha-hydroxysteroid dehydrogenase Function and homology information | |||||||||
Biological species | Brucella melitensis biotype 1 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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 | 8hsa.cif.gz | 354.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hsa.ent.gz | 291.9 KB | Display | PDB format |
PDBx/mmJSON format | 8hsa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hs/8hsa ftp://data.pdbj.org/pub/pdb/validation_reports/hs/8hsa | HTTPS FTP |
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-Related structure data
Related structure data | 8hdeC 8hdiC 8hdnC 8hs4C 8hs5C 8hs6C 8hs9C 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 25384.078 Da / Num. of mol.: 8 / Mutation: M196I/I258M/K262T Source method: isolated from a genetically manipulated source Details: Author stated: in our study, wild-type 7alpha-hydroxysteroid dehydrogenase (protein_id="QEX87556.1") from Brucella melis strain RM57(RM57CP044342.1) was cloned into E. coli. Sequence ...Details: Author stated: in our study, wild-type 7alpha-hydroxysteroid dehydrogenase (protein_id="QEX87556.1") from Brucella melis strain RM57(RM57CP044342.1) was cloned into E. coli. Sequence reference for strain RM57 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) Strain: RM57 / Gene: BMEI0406 / Production host: Escherichia coli (E. coli) References: UniProt: Q8YIN7, 7alpha-hydroxysteroid dehydrogenase #2: Chemical | ChemComp-NAD / 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: 2.33 Å3/Da / Density % sol: 47.24 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2M Sodium formate, 20% PEG ester 5000 |
-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: 3→23.84 Å / Num. obs: 68427 / % possible obs: 96.5 % / Redundancy: 3.8 % / Biso Wilson estimate: 39.3 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.134 / Rrim(I) all: 0.155 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 3→3.107 Å / Num. unique obs: 35933 / CC1/2: 0.885 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→23.84 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.99 / 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: 3→23.84 Å
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Refine LS restraints |
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LS refinement shell |
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