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Yorodumi- PDB-4nhx: Crystal structure of human OGFOD1, 2-oxoglutarate and iron-depend... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4nhx | ||||||
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Title | Crystal structure of human OGFOD1, 2-oxoglutarate and iron-dependent oxygenase domain containing 1, in complex with N-oxalylglycine (NOG) | ||||||
Components | 2-oxoglutarate and iron-dependent oxygenase domain-containing protein 1 | ||||||
Keywords | Oxidoreductase/Oxidoreductase inhibitor / jelly-roll fold / translation / ribosome / double-stranded beta helix / oxygen sensing / Oxidoreductase-Oxidoreductase inhibitor complex | ||||||
Function / homology | Function and homology information peptidyl-proline 3-dioxygenase activity / peptidyl-proline hydroxylation / protein hydroxylation / peptidyl-proline dioxygenase activity / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / regulation of translational termination / L-ascorbic acid binding / Protein hydroxylation / stress granule assembly / cytoplasmic stress granule ...peptidyl-proline 3-dioxygenase activity / peptidyl-proline hydroxylation / protein hydroxylation / peptidyl-proline dioxygenase activity / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / regulation of translational termination / L-ascorbic acid binding / Protein hydroxylation / stress granule assembly / cytoplasmic stress granule / cell population proliferation / iron ion binding / nucleoplasm / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.105 Å | ||||||
Authors | Horita, S. / McDonough, M.A. / Schofield, C.J. | ||||||
Citation | Journal: Structure / Year: 2015 Title: Structure of the Ribosomal Oxygenase OGFOD1 Provides Insights into the Regio- and Stereoselectivity of Prolyl Hydroxylases. Authors: Horita, S. / Scotti, J.S. / Thinnes, C. / Mottaghi-Taromsari, Y.S. / Thalhammer, A. / Ge, W. / Aik, W. / Loenarz, C. / Schofield, C.J. / McDonough, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nhx.cif.gz | 218.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nhx.ent.gz | 171.1 KB | Display | PDB format |
PDBx/mmJSON format | 4nhx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4nhx_validation.pdf.gz | 446.1 KB | Display | wwPDB validaton report |
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Full document | 4nhx_full_validation.pdf.gz | 446.7 KB | Display | |
Data in XML | 4nhx_validation.xml.gz | 19.6 KB | Display | |
Data in CIF | 4nhx_validation.cif.gz | 28.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nh/4nhx ftp://data.pdbj.org/pub/pdb/validation_reports/nh/4nhx | HTTPS FTP |
-Related structure data
Related structure data | 4nhkC 4nhlC 4nhmC 4nhyC 3kt7S 4nhn 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 , 1 types, 1 molecules A
#1: Protein | Mass: 65499.418 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: OGFOD1, KIAA1612, TPA1 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) References: UniProt: Q8N543, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor |
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-Non-polymers , 5 types, 179 molecules
#2: Chemical | ChemComp-MN / |
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#3: Chemical | ChemComp-NA / |
#4: Chemical | ChemComp-OGA / |
#5: Chemical | ChemComp-GOL / |
#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: 2.12 Å3/Da / Density % sol: 42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.7 mM MnCl2, 1.0 mM OGA, 25% (w/v) PEG 1500, 100 mM MIB buffer and 100 mM glycine, pH 6.5, 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 / Wavelength: 0.8344 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8344 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→50 Å / Num. all: 33393 / Num. obs: 33097 / % possible obs: 99.1 % / Redundancy: 16.2 % / Rmerge(I) obs: 0.153 / Net I/σ(I): 6.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 3KT7 Resolution: 2.105→45.239 Å / Occupancy max: 1 / Occupancy min: 0.32 / SU ML: 0.23 / Phase error: 24.37 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.7004 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.105→45.239 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1053→2.158 Å
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Refinement TLS params. | Method: refined / Origin x: -8.1162 Å / Origin y: 9.1731 Å / Origin z: 57.5758 Å
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Refinement TLS group |
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