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- PDB-2jgy: The crystal structure of human orotidine-5'-decarboxylase domain ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2jgy | ||||||
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Title | The crystal structure of human orotidine-5'-decarboxylase domain of human uridine monophosphate synthetase (UMPS) | ||||||
![]() | UMP SYNTHASE | ||||||
![]() | TRANSFERASE / GLYCOSYLTRANSFERASE / ALTERNATIVE SPLICING / LYASE / POLYMORPHISM / DECARBOXYLASE / DISEASE MUTATION / TIM BARREL DIMER / OROTIDINE-5'-DECARBOXYLASE / MULTIFUNCTIONAL ENZYME / PYRIMIDINE BIOSYNTHESIS | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Moche, M. / Ogg, D. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Dahlgren, L.G. / Edwards, A. / Ericsson, U.B. / Flodin, S. ...Moche, M. / Ogg, D. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Dahlgren, L.G. / Edwards, A. / Ericsson, U.B. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Holmberg-Schiavone, L. / Johansson, I. / Karlberg, T. / Kosinska, U. / Kotenyova, T. / Lehtio, L. / Nilsson, M.E. / Nyman, T. / Persson, C. / Sagemark, J. / Stenmark, P. / Sundstrom, M. / Uppenberg, J. / Upsten, M. / Thorsell, A.G. / van den Berg, S. / Weigelt, J. / Nordlund, P. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() Title: The Crystal Structure of Human Orotidine-5'-Decarboxylase Domain of Human Uridine Monophosphate Synthetase (Umps) Authors: Moche, M. / Flodin, S. / Nyman, T. / Stenmark, P. / Nordlund, P. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 122 KB | Display | ![]() |
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PDB format | ![]() | 95.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435.9 KB | Display | ![]() |
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Full document | ![]() | 440.1 KB | Display | |
Data in XML | ![]() | 26.9 KB | Display | |
Data in CIF | ![]() | 41.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1dqwS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 30631.232 Da / Num. of mol.: 2 Fragment: OROTIDINE-5'-DECARBOXYLASE DOMAIN OF UMPS, RESIDUES 224-479 Source method: isolated from a genetically manipulated source Details: THE FIRST TWO RESIDUES OF CHAIN A (SER222 AND MET223) ARE CLONING ARTIFACTS SINCE THEY BELONG TO THE N-TERMINAL LINKER BETWEEN THE START OF THE DECARBOXYLASE DOMAIN (GLU224) AND THE HEXAHISTIDINE TAIL Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P11172, orotidine-5'-phosphate decarboxylase #2: Water | ChemComp-HOH / | Sequence details | THE FIRST TWO RESIDUES OF CHAIN A (SER222 AND MET223) ARE CLONING ARTIFACTS SINCE THEY BELONG TO ...THE FIRST TWO RESIDUES OF CHAIN A (SER222 AND MET223) ARE CLONING ARTIFACTS SINCE THEY BELONG TO THE N-TERMINAL LINKER BETWEEN THE START OF THE DECARBOXYL | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 58 % |
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Crystal grow | pH: 7.5 / Details: pH 7.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 14, 2006 / Details: MULTILAYER MIRROR, CURVED TO FOCUS IN THE VERTICAL |
Radiation | Monochromator: BENT SILICON CRYSTAL, HORIZONTALLY FOCUSING. / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0408 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→25 Å / Num. obs: 58331 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 7.24 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 27 |
Reflection shell | Resolution: 1.95→2.07 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 10.4 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1DQW Resolution: 1.95→25 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.482 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THERE ARE TWO MOLECULES IN THE ASYMMETRIC UNIT, HOWEVER, NCS HAS NOT BEEN USED IN REFINEMENT.
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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: 21.67 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→25 Å
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Refine LS restraints |
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