+Open data
-Basic information
Entry | Database: PDB / ID: 2h8r | ||||||
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Title | Hepatocyte Nuclear Factor 1b bound to DNA: MODY5 Gene Product | ||||||
Components |
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Keywords | TRANSCRIPTION ACTIVATOR/DNA / trasncription factor / POU / homeo / protein-DNA / human disease / TRANSCRIPTION ACTIVATOR-DNA COMPLEX | ||||||
Function / homology | Function and homology information regulation of pronephros size / pronephric nephron tubule development / ureteric bud elongation / negative regulation of mesenchymal cell apoptotic process involved in mesonephric nephron morphogenesis / mesonephric duct formation / mesenchymal cell apoptotic process involved in metanephros development / hepatoblast differentiation / regulation of branch elongation involved in ureteric bud branching / negative regulation of mesenchymal cell apoptotic process involved in metanephros development / pronephros development ...regulation of pronephros size / pronephric nephron tubule development / ureteric bud elongation / negative regulation of mesenchymal cell apoptotic process involved in mesonephric nephron morphogenesis / mesonephric duct formation / mesenchymal cell apoptotic process involved in metanephros development / hepatoblast differentiation / regulation of branch elongation involved in ureteric bud branching / negative regulation of mesenchymal cell apoptotic process involved in metanephros development / pronephros development / Regulation of gene expression in early pancreatic precursor cells / inner cell mass cell differentiation / Nephron development / endodermal cell fate specification / embryonic digestive tract morphogenesis / endocrine pancreas development / genitalia development / hindbrain development / regulation of Wnt signaling pathway / pancreas development / insulin secretion / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / anterior/posterior pattern specification / branching morphogenesis of an epithelial tube / positive regulation of transcription initiation by RNA polymerase II / response to glucose / Notch signaling pathway / epithelial cell proliferation / kidney development / transcription coregulator binding / transcription regulator complex / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / intracellular membrane-bounded organelle / positive regulation of gene expression / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / DNA binding / nucleoplasm / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Lu, P. / Rha, G.B. / Chi, Y.I. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: Structural basis of disease-causing mutations in hepatocyte nuclear factor 1beta. Authors: Lu, P. / Rha, G.B. / Chi, Y.I. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2006 Title: Crystallization of hepatocyte nuclear factor 1beta in complex with DNA. Authors: Lu, P. / Li, Y. / Gorman, A. / Chi, Y.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2h8r.cif.gz | 131.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2h8r.ent.gz | 82.1 KB | Display | PDB format |
PDBx/mmJSON format | 2h8r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2h8r_validation.pdf.gz | 452.9 KB | Display | wwPDB validaton report |
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Full document | 2h8r_full_validation.pdf.gz | 665.8 KB | Display | |
Data in XML | 2h8r_validation.xml.gz | 40.4 KB | Display | |
Data in CIF | 2h8r_validation.cif.gz | 52.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h8/2h8r ftp://data.pdbj.org/pub/pdb/validation_reports/h8/2h8r | HTTPS FTP |
-Related structure data
Related structure data | 1ic8S 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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Details | Dimer when binding to DNA |
-Components
#1: DNA chain | Mass: 6107.977 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
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#2: DNA chain | Mass: 6157.016 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
#3: Protein | Mass: 25711.850 Da / Num. of mol.: 2 / Fragment: DNA Binding Domain (residues 91-310) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET41a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P35680 #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: 3.32 Å3/Da / Density % sol: 62.91 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 6%(v/v) PEG300, 5%(v/v) PEG8000, 8%(v/v) glycerol, 100mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.97923 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 18, 2005 |
Radiation | Monochromator: Rosenbaum-Rock monochromator high-resolution double-crystal Si (111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97923 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→27.9 Å / Num. all: 12635 / Num. obs: 12582 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 57.24 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.083 / Net I/σ(I): 28.8 |
Reflection shell | Resolution: 3.2→3.31 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 3.35 / Rsym value: 0.273 / % possible all: 63.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1IC8 Resolution: 3.2→20 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.829 / SU B: 21.564 / SU ML: 0.374 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.538 / 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: 69.209 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.201→3.282 Å / Total num. of bins used: 20
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