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Yorodumi- PDB-3ex6: D312N mutant of human orotidyl-5'-monophosphate decarboxylase in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ex6 | ||||||
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Title | D312N mutant of human orotidyl-5'-monophosphate decarboxylase in complex with 6-azido-UMP, covalent adduct | ||||||
Components | Orotidine-5'-phosphate decarboxylaseUridine monophosphate synthase | ||||||
Keywords | LYASE / decarboxylase / tim barrel / unusual catalysis / Disease mutation / Glycosyltransferase / Multifunctional enzyme / Pyrimidine biosynthesis / Transferase | ||||||
Function / homology | Function and homology information UMP biosynthetic process / orotate phosphoribosyltransferase / orotate phosphoribosyltransferase activity / pyrimidine nucleobase biosynthetic process / Pyrimidine biosynthesis / UDP biosynthetic process / orotidine-5'-phosphate decarboxylase / orotidine-5'-phosphate decarboxylase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process ...UMP biosynthetic process / orotate phosphoribosyltransferase / orotate phosphoribosyltransferase activity / pyrimidine nucleobase biosynthetic process / Pyrimidine biosynthesis / UDP biosynthetic process / orotidine-5'-phosphate decarboxylase / orotidine-5'-phosphate decarboxylase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / lactation / female pregnancy / cellular response to xenobiotic stimulus / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Heinrich, D. / Diederichsen, U. / Rudolph, M. | ||||||
Citation | Journal: Chemistry / Year: 2009 Title: Lys314 is a nucleophile in non-classical reactions of orotidine-5'-monophosphate decarboxylase Authors: Heinrich, D. / Diederichsen, U. / Rudolph, M.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ex6.cif.gz | 235.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ex6.ent.gz | 189.6 KB | Display | PDB format |
PDBx/mmJSON format | 3ex6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ex/3ex6 ftp://data.pdbj.org/pub/pdb/validation_reports/ex/3ex6 | HTTPS FTP |
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-Related structure data
Related structure data | 3ewuC 3ewwC 3ewxC 3ewyC 3ewzC 3ex1C 3ex2C 3ex3C 3ex4C 3l0kC 3l0nC 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 28298.758 Da / Num. of mol.: 2 / Fragment: UNP residues 224-480 / Mutation: D312N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UMPS / Plasmid: pETM-30 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) References: UniProt: P11172, orotidine-5'-phosphate decarboxylase |
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-Non-polymers , 5 types, 511 molecules
#2: Chemical | ChemComp-GOL / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-U5P / | #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: 2.45 Å3/Da / Density % sol: 49.86 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1 M Tris-HCl pH 8.0, 1.8 M (NH4)2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 300.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 9, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→44.68 Å / Num. obs: 131918 / % possible obs: 98 % / Redundancy: 7.3 % / Rsym value: 0.084 / Net I/σ(I): 7 |
Reflection shell | Resolution: 1.3→1.33 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.2 / Num. unique all: 4685 / Rsym value: 0.586 / % possible all: 76.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→44.68 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.427 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.052 / 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: 11.045 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→44.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.3→1.33 Å / Total num. of bins used: 20
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