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Yorodumi- PDB-4fne: X-ray Crystal structure of the Ancestral 3-keto steroid receptor ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fne | ||||||
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Title | X-ray Crystal structure of the Ancestral 3-keto steroid receptor - DOC complex | ||||||
Components | Steroid receptor 2Steroid hormone receptor | ||||||
Keywords | Steroid-Binding Protein / nuclear receptor / steroid receptor / hormone / DOC / deoxycorticosterone / cytosolic | ||||||
Function / homology | Retinoid X Receptor / Retinoid X Receptor / Orthogonal Bundle / Mainly Alpha / DESOXYCORTICOSTERONE Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.78 Å | ||||||
Authors | Ortlund, E.A. / Colucci, J.K. / Thornton, J. / Eick, G. / Harms, M. | ||||||
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 | 4fne.cif.gz | 68.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fne.ent.gz | 48.6 KB | Display | PDB format |
PDBx/mmJSON format | 4fne.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fn/4fne ftp://data.pdbj.org/pub/pdb/validation_reports/fn/4fne | HTTPS FTP |
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-Related structure data
Related structure data | 4fn9C 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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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 29199.818 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) |
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-Non-polymers , 6 types, 38 molecules
#2: Chemical | ChemComp-1CA / | ||||||||
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#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-MES / | #6: Chemical | ChemComp-CPS / | #7: 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: 3.3 Å3/Da / Density % sol: 62.71 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1M MES pH 6.0, glycerol, MgSO4, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 293.15 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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: Oct 9, 2008 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: SI(III) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.78→65.38 Å / Num. all: 9198 / Num. obs: 8757 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 72.12 Å2 / Rsym value: 0.071 / Net I/σ(I): 19.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: 1A28 Resolution: 2.78→65.38 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.888 / SU B: 18.631 / SU ML: 0.359 / Cross valid method: THROUGHOUT / ESU R: 1.634 / ESU R Free: 0.401 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 79.376 Å2
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Refinement step | Cycle: LAST / Resolution: 2.78→65.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.784→2.857 Å / Total num. of bins used: 20
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