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Yorodumi- PDB-4fn9: X-ray Crystal structure of the Ancestral 3-keto steroid receptor ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fn9 | ||||||
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Title | X-ray Crystal structure of the Ancestral 3-keto steroid receptor - Progesterone complex | ||||||
Components | Steroid receptor 2 | ||||||
Keywords | Steroid-Binding Protein / hormone / ancestral / Steroid Receptor / Nuclear Receptor / Progesterone Receptor / Cytosolic / nuclear | ||||||
Function / homology | Retinoid X Receptor / Retinoid X Receptor / Orthogonal Bundle / Mainly Alpha / PROGESTERONE Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Colucci, J.K. / Ortlund, E.A. / Thornton, J.W. | ||||||
Citation | Journal: PLoS Genet. / Year: 2012 Title: Evolution of minimal specificity and promiscuity in steroid hormone receptors. Authors: Eick, G.N. / Colucci, J.K. / Harms, M.J. / Ortlund, E.A. / Thornton, J.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fn9.cif.gz | 116.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fn9.ent.gz | 89.7 KB | Display | PDB format |
PDBx/mmJSON format | 4fn9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4fn9_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 4fn9_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 4fn9_validation.xml.gz | 24.6 KB | Display | |
Data in CIF | 4fn9_validation.cif.gz | 31.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fn/4fn9 ftp://data.pdbj.org/pub/pdb/validation_reports/fn/4fn9 | HTTPS FTP |
-Related structure data
Related structure data | 4fneC 1a28S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 29199.818 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Plasmid: LIC-MBP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) |
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-Non-polymers , 6 types, 22 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-SO4 / | #7: 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: 3.41 Å3/Da / Density % sol: 63.92 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 1.0M MgSO4, 10% glycerol, and 100 mM MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 1, 2008 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.73→49.63 Å / Num. all: 20584 / Num. obs: 21895 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rsym value: 0.089 / Net I/σ(I): 99.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1a28 Resolution: 3→49.604 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.917 / SU ML: 0.89 / σ(F): 1.34 / Phase error: 29.72 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.971 Å2 / ksol: 0.367 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3→49.604 Å
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Refine LS restraints |
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LS refinement shell |
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