+Open data
-Basic information
Entry | Database: PDB / ID: 2q1v | ||||||
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Title | Ancestral corticoid receptor in complex with cortisol | ||||||
Components | AncCR | ||||||
Keywords | TRANSCRIPTION / Nuclear Receptor / cortisol / corticoid / evolution / common ancestor / mineralocorticoid | ||||||
Function / homology | Retinoid X Receptor / Retinoid X Receptor / Orthogonal Bundle / Mainly Alpha / 17,21-DIHYDROXYPREGNA-1,4-DIENE-3,11,20-TRIONE Function and homology information | ||||||
Biological species | unidentified (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Ortlund, E.A. / Redinbo, M.R. | ||||||
Citation | Journal: Science / Year: 2007 Title: Crystal structure of an ancient protein: evolution by conformational epistasis. Authors: Ortlund, E.A. / Bridgham, J.T. / Redinbo, M.R. / 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 | 2q1v.cif.gz | 66.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2q1v.ent.gz | 48.2 KB | Display | PDB format |
PDBx/mmJSON format | 2q1v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q1/2q1v ftp://data.pdbj.org/pub/pdb/validation_reports/q1/2q1v | 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: 29052.707 Da / Num. of mol.: 1 / Mutation: C71S Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified (others) / Plasmid: pMALCH10T_AncCRLBD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21PlysS |
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#2: Chemical | ChemComp-PDN / |
#3: Chemical | ChemComp-GOL / |
#4: 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: 3.14 Å3/Da / Density % sol: 60.88 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: 9.5-15% PEG 3350, 5% glycerol, 50 mM Bis-Tris, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 295.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 14, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. all: 27636 / Num. obs: 27603 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Biso Wilson estimate: 20.8 Å2 / Rsym value: 0.089 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 5.5 / Num. unique all: 2702 / Rsym value: 0.375 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: AncCR Resolution: 1.95→46.56 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 121951.04 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.8628 Å2 / ksol: 0.375778 e/Å3 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.95→46.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.07 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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