+Open data
-Basic information
Entry | Database: PDB / ID: 2cgn | ||||||
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Title | FACTOR INHIBITING HIF-1 ALPHA with succinate | ||||||
Components | HYPOXIA-INDUCIBLE FACTOR 1 ALPHA INHIBITOR | ||||||
Keywords | OXIDOREDUCTASE / 2-OXOGLUTARATE / ACETYLATION / ACTIVATOR / ALTERNATIVE SPLICING / ASPARAGINYL HYDROXYLASE / DNA-BINDING / DSBH / FI / HIF / HYDROXYLATION / HYPOXIA / NUCLEAR PROTEIN / OXYGENASE / PHOSPHORYLATION / POLYMORPHISM / S-NITROSYLATION / TRANSCRIPTION / TRANSCRIPTION ACTIVATOR/INHIBITOR / TRANSCRIPTION REGULATION | ||||||
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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | McDonough, M.A. / Clifton, I.J. / Schofield, C.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Structural and Mechanistic Studies on the Inhibition of the Hypoxia-Inducible Transcription Factor Hydroxylases by Tricarboxylic Acid Cycle Intermediates. Authors: Hewitson, K. / Lienard, B. / McDonough, M.A. / Clifton, I.J. / Butler, D. / Soares, A.S. / Oldham, N.J. / McNeill, L.A. / Schofield, C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cgn.cif.gz | 84.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cgn.ent.gz | 63.3 KB | Display | PDB format |
PDBx/mmJSON format | 2cgn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cg/2cgn ftp://data.pdbj.org/pub/pdb/validation_reports/cg/2cgn | HTTPS FTP |
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-Related structure data
Related structure data | 2cgoC 1h2kS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 40328.281 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9NWT6, peptide-aspartate beta-dioxygenase | ||
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#2: Chemical | ChemComp-FE / | ||
#3: Chemical | ChemComp-SIN / | ||
#4: Chemical | ChemComp-SO4 / #5: 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: 3.49 Å3/Da / Density % sol: 65 % |
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Crystal grow | pH: 7.5 Details: 1.25M AMMONIUM SULFATE, 100MM HEPES PH7.5, 6% PEG400, 1MM IRON (II) SULFATE, 20MM SUCCINIC ACID, pH 7.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Aug 28, 2005 |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→34 Å / Num. obs: 767064 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 13.1 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 24.1 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 13 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 5.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1H2K Resolution: 2.4→74.54 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.922 / SU B: 14.859 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 0.298 / ESU R Free: 0.249 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.95 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→74.54 Å
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