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Yorodumi- PDB-1xu9: Crystal Structure of the Interface Closed Conformation of 11b-hyd... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xu9 | ||||||
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Title | Crystal Structure of the Interface Closed Conformation of 11b-hydroxysteroid dehydrogenase isozyme 1 | ||||||
Components | Corticosteroid 11-beta-dehydrogenase, isozyme 1 | ||||||
Keywords | OXIDOREDUCTASE / 11beta / hydroxysteroid / dehydrogenase / SDR | ||||||
Function / homology | Function and homology information 11beta-hydroxysteroid dehydrogenase / 11-beta-hydroxysteroid dehydrogenase (NADP+) activity / cortisol dehydrogenase activity / 7beta-hydroxysteroid dehydrogenase (NADP+) / 7-beta-hydroxysteroid dehydrogenase (NADP+) activity / Glucocorticoid biosynthesis / steroid catabolic process / Prednisone ADME / steroid binding / lung development ...11beta-hydroxysteroid dehydrogenase / 11-beta-hydroxysteroid dehydrogenase (NADP+) activity / cortisol dehydrogenase activity / 7beta-hydroxysteroid dehydrogenase (NADP+) / 7-beta-hydroxysteroid dehydrogenase (NADP+) activity / Glucocorticoid biosynthesis / steroid catabolic process / Prednisone ADME / steroid binding / lung development / NADP binding / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / protein homodimerization activity / membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.55 Å | ||||||
Authors | Hosfield, D.J. / Wu, Y. / Skene, R.J. / Hilger, M. / Jennings, A. / Snell, G.P. / Aertgeerts, K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Conformational Flexibility in Crystal Structures of Human 11beta-hydroxysteroid dehydrogenase type I provide insights into glucocorticoid interconversion and enzyme regulation. Authors: Hosfield, D.J. / Wu, Y. / Skene, R.J. / Hilger, M. / Jennings, A. / Snell, G.P. / Aertgeerts, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xu9.cif.gz | 253.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xu9.ent.gz | 202.2 KB | Display | PDB format |
PDBx/mmJSON format | 1xu9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xu/1xu9 ftp://data.pdbj.org/pub/pdb/validation_reports/xu/1xu9 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31836.875 Da / Num. of mol.: 4 / Mutation: C272S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HSD11B1, HSD11, HSD11L / Production host: Escherichia coli (E. coli) References: UniProt: P28845, 11beta-hydroxysteroid dehydrogenase #2: Chemical | ChemComp-NDP / #3: Chemical | ChemComp-CPS / #4: Chemical | ChemComp-MES / | #5: Water | ChemComp-HOH / | |
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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: 2.5 Å3/Da / Density % sol: 51 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7 Details: PEG, MES buffer, pH 7.0, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 1, 2003 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→20 Å / Num. all: 169082 / Num. obs: 169082 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.04 / Net I/σ(I): 20.9 |
Reflection shell | Resolution: 1.55→1.61 Å / Mean I/σ(I) obs: 2.2 / Rsym value: 0.314 / % possible all: 88.3 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.55→20 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.26 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.437 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 Å / Total num. of bins used: 20 /
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