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Yorodumi- PDB-4nr1: Factor inhibiting HIF-1 alpha in complex with consensus ankyrin r... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4nr1 | ||||||
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Title | Factor inhibiting HIF-1 alpha in complex with consensus ankyrin repeat domain-(d)allyl-GLY peptide | ||||||
Components |
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Keywords | OXIDOREDUCTASE / ON-HEME / DIOXYGENASE / OXYGENASE / DNA-BINDING / METAL-BINDING / TRANSCRIPTION / HELIX-LOOP-HELIX-BETA / DSBH / FACIAL TRIAD / ASPARAGINYL/ASPARTYL HYDROXYLASE / EPIGENETIC REGULATION / SIGNALING / ARD / BETA-HYDROXYLATION / ACTIVATOR-INHIBITOR / OXIDOREDUCTASE-PEPTIDE COMPLEX | ||||||
Function / homology | Function and homology information hypoxia-inducible factor-asparagine dioxygenase / : / [protein]-asparagine 3-dioxygenase activity / peptidyl-histidine dioxygenase activity / peptidyl-aspartic acid 3-dioxygenase activity / Cellular response to hypoxia / carboxylic acid binding / positive regulation of vasculogenesis / ankyrin repeat binding / oxygen sensor activity ...hypoxia-inducible factor-asparagine dioxygenase / : / [protein]-asparagine 3-dioxygenase activity / peptidyl-histidine dioxygenase activity / peptidyl-aspartic acid 3-dioxygenase activity / Cellular response to hypoxia / carboxylic acid binding / positive regulation of vasculogenesis / ankyrin repeat binding / oxygen sensor activity / Notch binding / negative regulation of Notch signaling pathway / NF-kappaB binding / positive regulation of myoblast differentiation / ferrous iron binding / transcription corepressor activity / perinuclear region of cytoplasm / protein homodimerization activity / zinc ion binding / nucleoplasm / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.68 Å | ||||||
Authors | Scotti, J.S. / McDonough, M.A. / Schofield, C.J. | ||||||
Citation | Journal: To be Published Title: Structure of an oxygenase in complex with substrate Authors: Scotti, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nr1.cif.gz | 157.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nr1.ent.gz | 122.4 KB | Display | PDB format |
PDBx/mmJSON format | 4nr1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4nr1_validation.pdf.gz | 465.9 KB | Display | wwPDB validaton report |
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Full document | 4nr1_full_validation.pdf.gz | 466.4 KB | Display | |
Data in XML | 4nr1_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 4nr1_validation.cif.gz | 20.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nr/4nr1 ftp://data.pdbj.org/pub/pdb/validation_reports/nr/4nr1 | HTTPS FTP |
-Related structure data
Related structure data | 4jaaC 1h2kS 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 / Protein/peptide , 2 types, 2 molecules AS
#1: Protein | Mass: 40610.551 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Strain: Homo sapiens / Gene: FIH1, HIF1AN / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9NWT6, hypoxia-inducible factor-asparagine dioxygenase |
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#2: Protein/peptide | Mass: 2215.546 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Non-polymers , 4 types, 59 molecules
#3: Chemical | ChemComp-ZN / | ||
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#4: Chemical | ChemComp-OGA / | ||
#5: Chemical | #6: 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: 3.24 Å3/Da / Density % sol: 62.01 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 1.6M AMMONIUM SULPHATE, 6% PEG 400, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 21, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Single bounce monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9173 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.68→74.69 Å / Num. all: 16485 / Num. obs: 16485 / % possible obs: 99.9 % / Redundancy: 10 % / Biso Wilson estimate: 54.683 Å2 / Rsym value: 0.1 / Net I/σ(I): 17.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1H2K Resolution: 2.68→74.69 Å / Occupancy max: 1 / Occupancy min: 1
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Displacement parameters | Biso max: 143.01 Å2 / Biso mean: 63.4135 Å2 / Biso min: 30 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.68→74.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.68→2.72 Å
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