+Open data
-Basic information
Entry | Database: PDB / ID: 6nj7 | ||||||
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Title | 11-BETA DEHYDROGENASE ISOZYME 1 IN COMPLEX WITH COLLETOIC ACID | ||||||
Components | Corticosteroid 11-beta-dehydrogenase isozyme 1 | ||||||
Keywords | OXIDOREDUCTASE / DEHYDROGENASE / INHIBITOR / COMPLEX / GLUCOCORTICOID REGULATION | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Miller, D.J. / Rivas, F. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2019 Title: Mechanistic Insight on the Mode of Action of Colletoic Acid. Authors: Ling, T. / Miller, D.J. / Lang, W.H. / Griffith, E. / Rodriguez-Cortes, A. / El Ayachi, I. / Palacios, G. / Min, J. / Miranda-Carboni, G. / Lee, R.E. / Rivas, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6nj7.cif.gz | 201.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nj7.ent.gz | 157.3 KB | Display | PDB format |
PDBx/mmJSON format | 6nj7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nj/6nj7 ftp://data.pdbj.org/pub/pdb/validation_reports/nj/6nj7 | HTTPS FTP |
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-Related structure data
Related structure data | 3d5qS 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
#1: Protein | Mass: 32175.279 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HSD11B1, HSD11, HSD11L, SDR26C1 Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others) References: UniProt: P28845, 11beta-hydroxysteroid dehydrogenase #2: Chemical | ChemComp-NAP / #3: Chemical | ChemComp-7H6 / ( #4: 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: 2.52 Å3/Da / Density % sol: 51.15 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: THE 4 UL DROP CONTAINED 2 UL PROTEIN (25 MM TRIS, PH 8.0, 250 MM NACL, 4 MM CHAPS, 10 MG/ML PROTEIN) AND 2 UL WELL SOLUTION (100 MM MES, PH 6.5, 20 PEG 4000), VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K PH range: 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 1, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→76.87 Å / Num. obs: 38505 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rsym value: 0.038 / Net I/σ(I): 2 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 5.1 % / Rsym value: 0.613 / % possible all: 89.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3D5Q Resolution: 2.6→76.87 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.935 / SU B: 17.24 / SU ML: 0.334 / Cross valid method: THROUGHOUT / ESU R: 0.583 / ESU R Free: 0.315 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 93.48 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→76.87 Å
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Refine LS restraints |
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