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Yorodumi- PDB-2eaw: Human UMP Synthase (C-terminal Domain- Orotidine 5'-Monophosphate... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2eaw | ||||||
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Title | Human UMP Synthase (C-terminal Domain- Orotidine 5'-Monophosphate Decarboxylase) | ||||||
Components | Uridine 5'-monophosphate synthase | ||||||
Keywords | LYASE / UMP synthase / C-terminal Domain / Orotidine 5'-Monophosphate Decarboxylase / human | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.88 Å | ||||||
Authors | Liu, Y. / Tang, H.L. / Pai, E.F. | ||||||
Citation | Journal: TO BE PUBLISHED Title: Human UMP Synthase (C-terminal Domain - Orotidine 5'-Monophosphate Decarboxylase) Authors: Liu, Y. / Tang, H.L. / Pai, E.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2eaw.cif.gz | 105.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2eaw.ent.gz | 80.6 KB | Display | PDB format |
PDBx/mmJSON format | 2eaw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ea/2eaw ftp://data.pdbj.org/pub/pdb/validation_reports/ea/2eaw | HTTPS FTP |
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-Related structure data
Related structure data | 1dqwS 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: 31751.604 Da / Num. of mol.: 2 Fragment: Orotidine 5'-Monophosphate Decarboxylase Domain, residues 1-291 (190-480) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UMPS / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS References: UniProt: P11172, orotidine-5'-phosphate decarboxylase, orotate phosphoribosyltransferase #2: Chemical | ChemComp-SO4 / | #3: 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: 2.01 Å3/Da / Density % sol: 38.96 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.4 Details: 2.28M Ammonium sulfate, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.54 Å |
Detector | Type: BRUKER SMART 6000 / Detector: CCD / Date: Feb 1, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.88→63.67 Å / Num. all: 11598 / Num. obs: 11348 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.84 % / Rmerge(I) obs: 0.1414 / Rsym value: 0.171 / Net I/σ(I): 4.29 |
Reflection shell | Resolution: 2.88→2.9 Å / Redundancy: 0.49 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.04 / Num. unique all: 232 / Rsym value: 0.5454 / % possible all: 28.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DQW Resolution: 2.88→63.63 Å / Cor.coef. Fo:Fc: 0.799 / Cor.coef. Fo:Fc free: 0.755 / SU B: 24.277 / SU ML: 0.482 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.564 / 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: 10.041 Å2
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Refinement step | Cycle: LAST / Resolution: 2.88→63.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.881→2.955 Å / Total num. of bins used: 20
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