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Yorodumi- PDB-2qcc: Crystal structure of the orotidine-5'-monophosphate decarboxylase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qcc | ||||||
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Title | Crystal structure of the orotidine-5'-monophosphate decarboxylase domain of human UMP synthase, apo form | ||||||
Components | Orotidine 5'- phosphate decarboxylase (OMPdecase) | ||||||
Keywords | LYASE / UMP synthase / decarboxylase / TIM barrel / catalytic proficiency | ||||||
Function / homology | Function and homology information UMP biosynthetic process / orotate phosphoribosyltransferase / orotate phosphoribosyltransferase activity / pyrimidine nucleobase biosynthetic process / Pyrimidine biosynthesis / orotidine-5'-phosphate decarboxylase / orotidine-5'-phosphate decarboxylase activity / UDP biosynthetic process / '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 / orotidine-5'-phosphate decarboxylase / orotidine-5'-phosphate decarboxylase activity / UDP biosynthetic process / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / lactation / female pregnancy / cellular response to xenobiotic stimulus / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Wittmann, J. / Rudolph, M. | ||||||
Citation | Journal: Structure / Year: 2008 Title: Structures of the human orotidine-5'-monophosphate decarboxylase support a covalent mechanism and provide a framework for drug design. Authors: Wittmann, J.G. / Heinrich, D. / Gasow, K. / Frey, A. / 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 | 2qcc.cif.gz | 113.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qcc.ent.gz | 87.7 KB | Display | PDB format |
PDBx/mmJSON format | 2qcc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2qcc_validation.pdf.gz | 465.3 KB | Display | wwPDB validaton report |
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Full document | 2qcc_full_validation.pdf.gz | 479 KB | Display | |
Data in XML | 2qcc_validation.xml.gz | 23.5 KB | Display | |
Data in CIF | 2qcc_validation.cif.gz | 33.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qc/2qcc ftp://data.pdbj.org/pub/pdb/validation_reports/qc/2qcc | HTTPS FTP |
-Related structure data
Related structure data | 2qcdC 2qceC 2qcfC 2qcgC 2qchC 2qclC 2qcmC 2qcnC 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: 28299.742 Da / Num. of mol.: 2 / Fragment: C-terminal domain 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): BL21 Rosetta 2(DE3) References: UniProt: P11172, orotidine-5'-phosphate decarboxylase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.49 Å3/Da / Density % sol: 50.51 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 Details: ammonium sulfate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5419 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 15, 2006 / Details: mirrors |
Radiation | Monochromator: filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5419 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→47 Å / Num. obs: 46969 / % possible obs: 94.3 % / Observed criterion σ(I): 0 / Redundancy: 10.8 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 28.5 |
Reflection shell | Resolution: 1.84→1.91 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 2 / Num. unique all: 2878 / Rsym value: 0.619 / % possible all: 58.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→46.96 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.926 / SU B: 8.308 / SU ML: 0.126 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.147 / ESU R Free: 0.151 / 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: 34.791 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→46.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.851→1.899 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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