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- PDB-3g3m: Crystal Structure of Human Orotidine 5'-monophosphate Decarboxyla... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3g3m | ||||||
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Title | Crystal Structure of Human Orotidine 5'-monophosphate Decarboxylase Covalently Modified by 5-fluoro-6-iodo-UMP | ||||||
![]() | Uridine 5'-monophosphate synthase | ||||||
![]() | LYASE / Human / Orotidine 5'-monophosphate Decarboxylase / c-terminal Domain / 5-fluoro-6-iodo-UMP / Alternative splicing / Decarboxylase / Disease mutation / Glycosyltransferase / Multifunctional enzyme / Phosphoprotein / Polymorphism / Pyrimidine biosynthesis / Transferase | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Liu, Y. / Tang, H.L. / Bello, A.M. / Poduch, E. / Kotra, L.P. / Pai, E.F. | ||||||
![]() | ![]() Title: Structure-activity relationships of orotidine-5'-monophosphate decarboxylase inhibitors as anticancer agents. Authors: Bello, A.M. / Konforte, D. / Poduch, E. / Furlonger, C. / Wei, L. / Liu, Y. / Lewis, M. / Pai, E.F. / Paige, C.J. / Kotra, L.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 77.2 KB | Display | ![]() |
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PDB format | ![]() | 55.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 750.9 KB | Display | ![]() |
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Full document | ![]() | 752 KB | Display | |
Data in XML | ![]() | 14.9 KB | Display | |
Data in CIF | ![]() | 22.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3g3dC ![]() 3s9yC ![]() 2p1fS C: citing same article ( 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 30488.162 Da / Num. of mol.: 1 Fragment: UNP residues 223-480, Orotidine 5'-phosphate decarboxylase domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P11172, orotidine-5'-phosphate decarboxylase |
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#2: Chemical | ChemComp-5FU / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.06 % |
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Crystal grow | Temperature: 293 K / 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: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 16, 2007 Details: DCM WITH CRYO-COOLED 1ST CRYSTAL SAGITTALLY BENT 2ND CRYSTAL FOLLOWED BY VERTICALLY FOCUSING MIRROR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. obs: 50630 / % possible obs: 93.1 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.213 / Mean I/σ(I) obs: 3.5 / Rsym value: 0.213 / % possible all: 60.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2P1F Resolution: 1.4→50 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / SU B: 0.869 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.06 / 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: 15.312 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.44 Å / Total num. of bins used: 20
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