[English] 日本語
Yorodumi- PDB-6m9u: Structure of the apo-form of 20beta-Hydroxysteroid Dehydrogenase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6m9u | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the apo-form of 20beta-Hydroxysteroid Dehydrogenase from Bifidobacterium adolescentis strain L2-32 | ||||||
Components | Oxidoreductase, short chain dehydrogenase/reductase family protein | ||||||
Keywords | OXIDOREDUCTASE / pyridine nucleotide-dependent enzyme / short-chain dehydrogenase/reductase / NADH dependent | ||||||
Function / homology | Function and homology information Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Bifidobacterium adolescentis L2-32 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Mythen, S.M. / Pollet, R.M. / Koropatkin, N.M. / Ridlon, J.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2019 Title: Structural and biochemical characterization of 20 beta-hydroxysteroid dehydrogenase fromBifidobacterium adolescentisstrain L2-32. Authors: Doden, H.L. / Pollet, R.M. / Mythen, S.M. / Wawrzak, Z. / Devendran, S. / Cann, I. / Koropatkin, N.M. / Ridlon, J.M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6m9u.cif.gz | 207.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6m9u.ent.gz | 169.3 KB | Display | PDB format |
PDBx/mmJSON format | 6m9u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6m9u_validation.pdf.gz | 515.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6m9u_full_validation.pdf.gz | 525.7 KB | Display | |
Data in XML | 6m9u_validation.xml.gz | 23.7 KB | Display | |
Data in CIF | 6m9u_validation.cif.gz | 32.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m9/6m9u ftp://data.pdbj.org/pub/pdb/validation_reports/m9/6m9u | HTTPS FTP |
-Related structure data
Related structure data | 6ow4C 3r1iS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 30522.064 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bifidobacterium adolescentis L2-32 (bacteria) Gene: BIFADO_01909 / Production host: Escherichia coli (E. coli) / References: UniProt: A7A7R9 |
---|
-Non-polymers , 9 types, 194 molecules
#2: Chemical | #3: Chemical | ChemComp-MES / | #4: Chemical | ChemComp-EDO / #5: Chemical | #6: Chemical | ChemComp-PEG / #7: Chemical | ChemComp-PG4 / | #8: Chemical | ChemComp-CL / | #9: Chemical | #10: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.69 Å3/Da / Density % sol: 70.42 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 20% v/v 2-propanol, 0.1 M MES monohydrate pH 6.0, 20% w/v Polyethylene glycol monomethyl ether 2,000 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.979 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 28, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50.69 Å / Num. obs: 338597 / % possible obs: 99.57 % / Redundancy: 7.3 % / Biso Wilson estimate: 41.11 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1402 / Rpim(I) all: 0.05497 / Rrim(I) all: 0.1509 / Net I/σ(I): 9.52 |
Reflection shell | Resolution: 2.2→2.279 Å / Num. unique obs: 33468 / % possible all: 99.72 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3R1I Resolution: 2.2→50.686 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.11
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 232.73 Å2 / Biso mean: 65.9959 Å2 / Biso min: 27.37 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→50.686 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27
|