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Yorodumi- PDB-2xum: FACTOR INHIBITING HIF (FIH) Q239H MUTANT IN COMPLEX WITH ZN(II), ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xum | ||||||
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Title | FACTOR INHIBITING HIF (FIH) Q239H MUTANT IN COMPLEX WITH ZN(II), NOG AND ASP-SUBSTRATE PEPTIDE (20-MER) | ||||||
Components |
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Keywords | OXIDOREDUCTASE/PEPTIDE / OXIDOREDUCTASE-PEPTIDE COMPLEX / NON-HEME / DIOXYGENASE / OXYGENASE / HYPOXIA / METAL-BINDING / HELIX-LOOP-HELIX-BETA / FACIAL TRIAD SIGNALING / BETA-HYDROXYLATION / TRANSCRIPTION ACTIVATOR/INHIBITOR | ||||||
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 / negative regulation of DNA-binding transcription factor activity / perinuclear region of cytoplasm / protein homodimerization activity / zinc ion binding / nucleoplasm / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) SYNTHETIC CONSTRUCT (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Chowdhury, R. / McDonough, M.A. / Schofield, C.J. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2011 Title: Asparagine and aspartate hydroxylation of the cytoskeletal ankyrin family is catalyzed by factor-inhibiting hypoxia-inducible factor. Authors: Yang, M. / Ge, W. / Chowdhury, R. / Claridge, T.D. / Kramer, H.B. / Schmierer, B. / McDonough, M.A. / Gong, L. / Kessler, B.M. / Ratcliffe, P.J. / Coleman, M.L. / Schofield, C.J. #1: Journal: J.Biol.Chem. / Year: 2007 Title: Asparaginyl Hydroxylation of the Notch Ankyrin Repeat Domain by Factor Inhibiting Hypoxia-Inducible Factor. Authors: Coleman, M.L. / McDonough, M.A. / Hewitson, K.S. / Coles, C. / Mecinovic, J. / Edelmann, M. / Cook, K.M. / Cockman, M.E. / Lancaster, D.E. / Kessler, B.M. / Oldham, N.J. / Ratcliffe, P.J. / 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 | 2xum.cif.gz | 92 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xum.ent.gz | 68.5 KB | Display | PDB format |
PDBx/mmJSON format | 2xum.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xu/2xum ftp://data.pdbj.org/pub/pdb/validation_reports/xu/2xum | HTTPS FTP |
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-Related structure data
Related structure data | 1h2kS 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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2 |
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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 2 molecules AS
#1: Protein | Mass: 40338.297 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q9NWT6, peptide-aspartate beta-dioxygenase |
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#2: Protein/peptide | Mass: 2233.519 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: BASED ON BIOLOGICAL SEQUENCE / Source: (synth.) SYNTHETIC CONSTRUCT (others) |
-Non-polymers , 4 types, 159 molecules
#3: Chemical | ChemComp-ZN / | ||
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#4: Chemical | ChemComp-OGA / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Compound details | ENGINEEREDNonpolymer details | RESIDUE OGA IS THE N-OXALYL GLYCINE (NOG). | |
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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: 3.22 Å3/Da / Density % sol: 62 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 7.5 Details: 1.6M AMMONIUM SULPHATE, 6% PEG400, 0.1M HEPES PH7.5, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 25, 2010 / Details: MIRRORS |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→74.12 Å / Num. obs: 26863 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 9.2 % / Biso Wilson estimate: 51.7 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 28.5 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 2.23 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1H2K Resolution: 2.2→74.12 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.948 / SU B: 11.189 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.172 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.924 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→74.12 Å
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Refine LS restraints |
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