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Yorodumi- PDB-3dbp: Crystal Structure of Human Orotidine 5'-Monophosphate Decarboxyla... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dbp | ||||||
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Title | Crystal Structure of Human Orotidine 5'-Monophosphate Decarboxylase Complexed with 6-NH2-UMP | ||||||
Components | Orotidine 5'-phosphate decarboxylase | ||||||
Keywords | LYASE / Human / UMP Synthase / Orotidine 5'-Monophosphate Decarboxylase / 6-NH2-UMP / Alternative splicing / Decarboxylase / Disease mutation / Glycosyltransferase / Multifunctional enzyme / Polymorphism / Pyrimidine biosynthesis / Transferase | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Liu, Y. / To, T. / Bello, A.M. / Kotra, L.P. / Pai, E.F. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Human Orotidine 5'-Monophosphate Decarboxylase Complexed with 6-NH2-UMP Authors: Liu, Y. / To, T. / Bello, A.M. / Kotra, L.P. / 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 | 3dbp.cif.gz | 127.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dbp.ent.gz | 98.4 KB | Display | PDB format |
PDBx/mmJSON format | 3dbp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3dbp_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 3dbp_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3dbp_validation.xml.gz | 25.3 KB | Display | |
Data in CIF | 3dbp_validation.cif.gz | 37.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/db/3dbp ftp://data.pdbj.org/pub/pdb/validation_reports/db/3dbp | HTTPS FTP |
-Related structure data
Related structure data | 2p1fS 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: 30472.162 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UMPS, OK/SW-cl.21 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS References: UniProt: P11172, orotidine-5'-phosphate decarboxylase #2: Chemical | #3: Chemical | #4: 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: 2.27 Å3/Da / Density % sol: 45.85 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.4 Details: 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: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.978654 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 28, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978654 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. all: 87460 / Num. obs: 84448 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 4 / Num. unique all: 8669 / Rsym value: 0.293 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2P1F Resolution: 1.5→18.67 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.085 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.068 / ESU R Free: 0.069 / 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: 16.255 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→18.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.538 Å / Total num. of bins used: 20
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