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Yorodumi- PDB-6gbt: 17beta-hydroxysteroid dehydrogenase type 14 Mutant Y253A in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gbt | ||||||
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Title | 17beta-hydroxysteroid dehydrogenase type 14 Mutant Y253A in complex with a non-steroidal inhibitor | ||||||
Components | 17-beta-hydroxysteroid dehydrogenase 14 | ||||||
Keywords | OXIDOREDUCTASE / Inhibitor Complex mutant | ||||||
Function / homology | Function and homology information Estrogen biosynthesis / testosterone 17-beta-dehydrogenase (NADP+) activity / 17beta-estradiol 17-dehydrogenase / estradiol 17-beta-dehydrogenase [NAD(P)+] activity / steroid catabolic process / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Badran, M. / Klebe, G. / Heine, A. / Marchais-Oberwinkler, S. | ||||||
Citation | Journal: To Be Published Title: 17beta Hydroxysteroid Dehydrogenase type 14 mutant C255A in complex with non-steroidal inhibitor Authors: Badran, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gbt.cif.gz | 68.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gbt.ent.gz | 48.5 KB | Display | PDB format |
PDBx/mmJSON format | 6gbt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6gbt_validation.pdf.gz | 1012.1 KB | Display | wwPDB validaton report |
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Full document | 6gbt_full_validation.pdf.gz | 1012.3 KB | Display | |
Data in XML | 6gbt_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | 6gbt_validation.cif.gz | 18.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gb/6gbt ftp://data.pdbj.org/pub/pdb/validation_reports/gb/6gbt | HTTPS FTP |
-Related structure data
Related structure data | 5icmS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 28297.330 Da / Num. of mol.: 1 / Mutation: C255A Source method: isolated from a genetically manipulated source Details: Wild type S205 PubMed:10800688mutation Cys255Ala / Source: (gene. exp.) Homo sapiens (human) / Gene: HSD17B14, DHRS10, SDR3, SDR47C1, UNQ502/PRO474 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold pLysS AG References: UniProt: Q9BPX1, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor |
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-Non-polymers , 5 types, 163 molecules
#2: Chemical | ChemComp-NAD / |
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#3: Chemical | ChemComp-F45 / [ |
#4: Chemical | ChemComp-DMS / |
#5: Chemical | ChemComp-NA / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.06 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG6000 50% W/V HEPES 0.1M DMSO 5% / PH range: 6.5 - 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 26, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 17086 / % possible obs: 99.4 % / Redundancy: 8.7 % / CC1/2: 0.999 / Rrim(I) all: 0.093 / Rsym value: 0.087 / Net I/σ(I): 20.84 |
Reflection shell | Resolution: 2.1→2.22 Å / Redundancy: 9 % / Mean I/σ(I) obs: 4.75 / Num. unique obs: 2653 / CC1/2: 0.928 / Rrim(I) all: 0.506 / Rsym value: 0.477 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5icm Resolution: 2.1→46.5989 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.31
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→46.5989 Å
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Refine LS restraints |
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LS refinement shell |
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