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- PDB-8hde: Brucella melitensis 7-alpha-Hydroxysteroid Dehydrogenase mutant: ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8hde | |||||||||
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Title | Brucella melitensis 7-alpha-Hydroxysteroid Dehydrogenase mutant: 1-53 truncation/I258M | |||||||||
![]() | 7-alpha-hydroxysteroid dehydrogenase | |||||||||
![]() | OXIDOREDUCTASE / SDR family / hydroxysteroid dehydrogenase | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Liu, Z.Y. / Zhang, R.Z. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of 7-alpha-hydroxysteroid dehydrogenase Authors: Liu, Z.Y. / Zhang, R.Z. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 102 KB | Display | ![]() |
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PDB format | ![]() | 76.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8hdiC ![]() 8hdnC ![]() 8hs4C ![]() 8hs5C ![]() 8hs6C ![]() 8hs9C ![]() 8hsaC ![]() 1fmcS ![]() 3gafS S: Starting model for refinement C: citing same article ( |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 25769.514 Da / Num. of mol.: 2 / Fragment: 1-53 truncation / Mutation: I258M Source method: isolated from a genetically manipulated source Details: Sequence reference for Brucella melitensis is not available in UniProt at the time of biocuration. Current sequence reference is from GenBank id QEX87556.1. Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.8 % / Description: orthorhombic |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 0.1M MIB buffer, 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: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1 Å |
Detector | Type: Bruker PHOTON III / Detector: PIXEL / Date: Dec 7, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→23.6 Å / Num. obs: 27394 / % possible obs: 99.6 % / Redundancy: 10 % / CC1/2: 0.996 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.05 / Rrim(I) all: 0.158 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.7→2.79 Å / Num. unique obs: 14529 / CC1/2: 0.996 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3GAF,1FMC Resolution: 2.7→23.6 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.27 / 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: 2.7→23.6 Å
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Refine LS restraints |
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LS refinement shell |
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