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Yorodumi- PDB-2v30: Human orotidine 5'-phosphate decarboxylase domain of uridine mono... -
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-Basic information
Entry | Database: PDB / ID: 2v30 | ||||||
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Title | Human orotidine 5'-phosphate decarboxylase domain of uridine monophospate synthetase (UMPS) in complex with its product UMP. | ||||||
Components | OROTIDINE 5'-PHOSPHATE DECARBOXYLASE | ||||||
Keywords | LYASE / ALTERNATIVE SPLICING / PYRIMIDINE METABOLISM / DISEASE MUTATION / GLYCOSYLTRANSFERASE / UMP / TRANSFERASE / POLYMORPHISM / DECARBOXYLASE / MULTIFUNCTIONAL ENZYME / PYRIMIDINE BIOSYNTHESIS | ||||||
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: 2 Å | ||||||
Authors | Moche, M. / Ogg, D. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Dahlgren, L.G. / Edwards, A. / Flodin, S. / Flores, A. ...Moche, M. / Ogg, D. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Dahlgren, L.G. / Edwards, A. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Holmberg-Schiavone, L. / Johansson, I. / Kallas, A. / Karlberg, T. / Kotenyova, T. / Lehtio, L. / Nyman, T. / Persson, C. / Sagemark, J. / Stenmark, P. / Sundstrom, M. / Thorsell, A.G. / van den Berg, S. / Weigelt, J. / Welin, M. / Nordlund, P. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: The Crystal Structure of Human Orotidine 5'-Decarboxylase Domain of Human Uridine Monophosphate Synthetase (Umps) Authors: Moche, M. / Ogg, D. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Dahlgren, L.G. / Edwards, A. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / ...Authors: Moche, M. / Ogg, D. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Dahlgren, L.G. / Edwards, A. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Holmberg-Schiavone, L. / Johansson, I. / Kallas, A. / Karlberg, T. / Kotenyova, T. / Lehtio, L. / Nyman, T. / Persson, C. / Sagemark, J. / Stenmark, P. / Sundstrom, M. / Thorsell, A.G. / van den Berg, S. / Weigelt, J. / Welin, M. / 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 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v30.cif.gz | 131.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v30.ent.gz | 101.5 KB | Display | PDB format |
PDBx/mmJSON format | 2v30.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v3/2v30 ftp://data.pdbj.org/pub/pdb/validation_reports/v3/2v30 | HTTPS FTP |
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-Related structure data
Related structure data | 2jgyS 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.8426, 0.07993, -0.5326), Vector: |
-Components
#1: Protein | Mass: 30631.232 Da / Num. of mol.: 2 Fragment: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE DOMAIN, RESIDUES 224-479 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Description: MAMMALIAN GENE COLLECTION (MGC) / Plasmid: PNIC-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P11172, orotidine-5'-phosphate decarboxylase #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT CONTAINS A HEXAHISTIDINE TAG AND A LINKER SEQUENCE IN THE N-TERMINUS. THE CONSTRUCT ...THE CONSTRUCT CONTAINS A HEXAHISTID | |
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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: 2.65 Å3/Da / Density % sol: 53.28 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.00595 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 1, 2007 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00595 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 49400 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 14.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 35.6 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 14.4 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 12.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2JGY Resolution: 2→19.64 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.688 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.123 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.42 Å2
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Refinement step | Cycle: LAST / Resolution: 2→19.64 Å
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