[English] 日本語
Yorodumi- PDB-1fdw: HUMAN 17-BETA-HYDROXYSTEROID-DEHYDROGENASE TYPE 1 MUTANT H221Q CO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fdw | ||||||
---|---|---|---|---|---|---|---|
Title | HUMAN 17-BETA-HYDROXYSTEROID-DEHYDROGENASE TYPE 1 MUTANT H221Q COMPLEXED WITH ESTRADIOL | ||||||
Components | 17-BETA-HYDROXYSTEROID DEHYDROGENASE | ||||||
Keywords | DEHYDROGENASE / 17-BETA-HYDROXYSTEROID / MUTANT / ESTRADIOL / NADP | ||||||
Function / homology | Function and homology information estradiol binding / 3(or 17)beta-hydroxysteroid dehydrogenase / 17-beta-hydroxysteroid dehydrogenase (NADP+) activity / estrogen biosynthetic process / testosterone dehydrogenase [NAD(P)+] activity / cellular response to metal ion / Estrogen biosynthesis / dihydrotestosterone 17-beta-dehydrogenase activity / testosterone biosynthetic process / testosterone dehydrogenase (NAD+) activity ...estradiol binding / 3(or 17)beta-hydroxysteroid dehydrogenase / 17-beta-hydroxysteroid dehydrogenase (NADP+) activity / estrogen biosynthetic process / testosterone dehydrogenase [NAD(P)+] activity / cellular response to metal ion / Estrogen biosynthesis / dihydrotestosterone 17-beta-dehydrogenase activity / testosterone biosynthetic process / testosterone dehydrogenase (NAD+) activity / testosterone 17-beta-dehydrogenase (NADP+) activity / 17beta-estradiol 17-dehydrogenase / estradiol 17-beta-dehydrogenase [NAD(P)+] activity / steroid biosynthetic process / estrogen metabolic process / NADP+ binding / lysosome organization / The canonical retinoid cycle in rods (twilight vision) / small molecule binding / catalytic activity / adipose tissue development / skeletal muscle tissue development / steroid binding / bone development / NADP binding / gene expression / protein homodimerization activity / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Mazza, C. / Breton, R. / Housset, D. / Fontecilla-Camps, J.-C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1998 Title: Unusual charge stabilization of NADP+ in 17beta-hydroxysteroid dehydrogenase. Authors: Mazza, C. / Breton, R. / Housset, D. / Fontecilla-Camps, J.C. #1: Journal: Thesis, Universite Joseph Fourier / Year: 1997 Title: Human Type I 17Beta-Hydroxysteroid Dehydrogenase: Site Directed Mutagenesis and X-Ray Crystallography Structure-Function Analysis Authors: Mazza, C. #2: Journal: Structure / Year: 1996 Title: The Structure of a Complex of Human 17Beta-Hydroxysteroid Dehydrogenase with Estradiol and Nadp+ Identifies Two Principal Targets for the Design of Inhibitors Authors: Breton, R. / Housset, D. / Mazza, C. / Fontecilla-Camps, J.C. #3: Journal: Structure / Year: 1995 Title: Structure of Human Estrogenic 17 Beta-Hydroxysteroid Dehydrogenase at 2.20 A Resolution Authors: Ghosh, D. / Pletnev, V.Z. / Zhu, D.W. / Wawrzak, Z. / Duax, W.L. / Pangborn, W. / Labrie, F. / Lin, S.X. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1fdw.cif.gz | 65.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1fdw.ent.gz | 48.5 KB | Display | PDB format |
PDBx/mmJSON format | 1fdw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fdw_validation.pdf.gz | 648 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1fdw_full_validation.pdf.gz | 658.3 KB | Display | |
Data in XML | 1fdw_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 1fdw_validation.cif.gz | 17 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fd/1fdw ftp://data.pdbj.org/pub/pdb/validation_reports/fd/1fdw | HTTPS FTP |
-Related structure data
Related structure data | 1fduC 1fdvC 1fdtS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 34963.930 Da / Num. of mol.: 1 / Mutation: H221Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOPLASM / Plasmid: PVL1393 / Cellular location (production host): CYTOPLASM / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P14061, 17beta-estradiol 17-dehydrogenase |
---|---|
#2: Chemical | ChemComp-EST / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 7 Details: PROTEIN WAS CRYSTALLIZED FROM PEG 4000 30%, 100 MM HEPES BUFFER PH 7.0, 100 MM MGCL2, 0.5 MM ESTRADIOL, PROPANE DIOL 2-4% | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 300 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Date: Apr 1, 1994 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→35.8 Å / Num. obs: 6352 / % possible obs: 65.2 % / Observed criterion σ(I): 0 / Redundancy: 2.54 % / Rsym value: 0.071 |
Reflection shell | Resolution: 2.7→2.83 Å |
Reflection | *PLUS Rmerge(I) obs: 0.071 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FDT Resolution: 2.7→10 Å / σ(F): 2 Details: THE LOOP 191 - 197 HAS BEEN EXCLUDED FROM THE COORDINATE FILE.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.29 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→10 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.178 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |