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Yorodumi- PDB-3p0u: Crystal Structure of the ligand binding domain of human testicula... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3p0u | ||||||
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Title | Crystal Structure of the ligand binding domain of human testicular receptor 4 | ||||||
Components | Nuclear receptor subfamily 2 group C member 2 | ||||||
Keywords | SIGNALING PROTEIN / Ligand binding domain / Orphan nuclear receptor / testicular receptor 4 | ||||||
Function / homology | Function and homology information positive regulation of embryonic development / anatomical structure development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / nervous system development / spermatogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding ...positive regulation of embryonic development / anatomical structure development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / nervous system development / spermatogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Zhou, X.E. / Suino-Powell, K.M. / Xu, Y. / Chan, C.-W. / Kruse, S.W. / Reynolds, R. / Engel, J.D. / Xu, H.E. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: The Orphan Nuclear Receptor TR4 Is a Vitamin A-activated Nuclear Receptor. Authors: Zhou, X.E. / Suino-Powell, K.M. / Xu, Y. / Chan, C.W. / Tanabe, O. / Kruse, S.W. / Reynolds, R. / Engel, J.D. / Xu, H.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3p0u.cif.gz | 186 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3p0u.ent.gz | 151.3 KB | Display | PDB format |
PDBx/mmJSON format | 3p0u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p0/3p0u ftp://data.pdbj.org/pub/pdb/validation_reports/p0/3p0u | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28102.188 Da / Num. of mol.: 2 / Fragment: Ligand binding domain / Mutation: K539A, K550A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NR2C2, TAK1, TR4 / Production host: Escherichia coli (E. coli) / References: UniProt: P49116 #2: 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: 3.75 Å3/Da / Density % sol: 67.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2M (NH4)2SO4, 0.1M HEPES, 25% w/v PEG 3,350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å | ||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 15, 2008 | ||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||
Reflection | Resolution: 3→50 Å / Num. obs: 17576 / % possible obs: 92.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.3 % / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 25.2 | ||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→30 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.915 / SU B: 41.216 / SU ML: 0.337 / Cross valid method: THROUGHOUT / ESU R Free: 0.419 / 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: 72.439 Å2
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Refinement step | Cycle: LAST / Resolution: 3→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.077 Å / Total num. of bins used: 20
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