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- PDB-2qcf: Crystal structure of the orotidine-5'-monophosphate decarboxylase... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2qcf | ||||||
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Title | Crystal structure of the orotidine-5'-monophosphate decarboxylase domain (Asp312Asn mutant) of human UMP synthase bound to 5-fluoro-UMP | ||||||
![]() | Uridine 5'-monophosphate synthase (UMP synthase) | ||||||
![]() | LYASE / UMP synthase / decarboxylase / catalytic proficiency | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wittmann, J. / Rudolph, M. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 135.1 KB | Display | ![]() |
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PDB format | ![]() | 111 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 747.9 KB | Display | ![]() |
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Full document | ![]() | 753 KB | Display | |
Data in XML | ![]() | 16.9 KB | Display | |
Data in CIF | ![]() | 26.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2qccC ![]() 2qcdC ![]() 2qceC ![]() 2qcgC ![]() 2qchC ![]() 2qclC ![]() 2qcmC ![]() 2qcnC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 28330.824 Da / Num. of mol.: 1 / Fragment: C-terminal domain / Mutation: y Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P11172, orotidine-5'-phosphate decarboxylase |
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#2: Chemical | ChemComp-5FU / |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.85 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 Details: pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 28, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.22→22.14 Å / Num. obs: 81404 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rsym value: 0.083 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 1.22→1.24 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 3900 / Rsym value: 0.594 |
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Processing
Software | Name: REFMAC / Version: 5.2.0019 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The atoms that are in close contact have occupancy less than 1 and are mutually exclusive.
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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: 9.11 Å2
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Refinement step | Cycle: LAST / Resolution: 1.22→22.14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.22→1.25 Å / Total num. of bins used: 20
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