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Yorodumi- PDB-2wns: Human Orotate phosphoribosyltransferase (OPRTase) domain of Uridi... -
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-Basic information
Entry | Database: PDB / ID: 2wns | ||||||
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Title | Human Orotate phosphoribosyltransferase (OPRTase) domain of Uridine 5' -monophosphate synthase (UMPS) in complex with its substrate orotidine 5'-monophosphate (OMP) | ||||||
Components | OROTATE PHOSPHORIBOSYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / ALTERNATIVE SPLICING / MULTIFUNCTIONAL ENZYME / LYASE / POLYMORPHISM / DECARBOXYLASE / PHOSPHOPROTEIN / DISEASE MUTATION / GLYCOSYLTRANSFERASE / 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: 1.9 Å | ||||||
Authors | Moche, M. / Roos, A. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. ...Moche, M. / Roos, A. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Karlberg, T. / Kotyenova, T. / Kotzch, A. / Nielsen, T.K. / Nyman, T. / Persson, C. / Sagemark, J. / Schueler, H. / Schutz, P. / Siponen, M.I. / Svensson, L. / Thorsell, A.G. / Tresaugues, L. / VanDenBerg, S. / Weigelt, J. / Welin, M. / Wisniewska, M. / Nordlund, P. | ||||||
Citation | Journal: To be Published Title: Human Orotate Phosphoribosyltransferase (Oprtase) Domain of Uridine 5'-Monophosphate Synthase (Umps) in Complex with its Substrate Orotidine 5'-Monophosphate (Omp) Authors: Moche, M. / Roos, A. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. ...Authors: Moche, M. / Roos, A. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Karlberg, T. / Kotyenova, T. / Kotzch, A. / Nielsen, T.K. / Nyman, T. / Persson, C. / Sagemark, J. / Schueler, H. / Schutz, P. / Siponen, M.I. / Svensson, L. / Thorsell, A.G. / Tresaugues, L. / Vandenberg, S. / Weigelt, J. / Welin, M. / Wisniewska, M. / Nordlund, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wns.cif.gz | 94 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wns.ent.gz | 71.9 KB | Display | PDB format |
PDBx/mmJSON format | 2wns.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wn/2wns ftp://data.pdbj.org/pub/pdb/validation_reports/wn/2wns | HTTPS FTP |
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-Related structure data
Related structure data | 2zykS 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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-Components
#1: Protein | Mass: 22615.191 Da / Num. of mol.: 2 / Fragment: OPRTASE DOMAIN, RESIDUES 7-203 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-CH2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) R3 PRARE References: UniProt: P11172, orotate phosphoribosyltransferase #2: Chemical | #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | Nonpolymer details | OROTIDINE-5'-MONOPHOSPHATE (OMP): THE OROTIDINE 5-MONOPHOSPHATE, OMP, WAS RENAMED INTO DRG SINCE ...OROTIDINE-5'-MONOPHOSPH | Sequence details | THE SEQUENCE CONTAINS ONLY THE OROTATE PHOSPHORIBOSYLTRANSFERASE DOMAIN OF UMPS AND IS FURTHER CUT ...THE SEQUENCE CONTAINS ONLY THE OROTATE PHOSPHORIB | |
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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: 1.95 Å3/Da / Density % sol: 36.52 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9793 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jan 30, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→37.06 Å / Num. obs: 28358 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 4 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 3.6 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ZYK Resolution: 1.9→37.06 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.909 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.155 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.51 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→37.06 Å
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