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- PDB-3ex1: human orotidyl-5'-monophosphate decarboxylase soaked with 6-cyano... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ex1 | ||||||
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Title | human orotidyl-5'-monophosphate decarboxylase soaked with 6-cyano-UMP, converted to UMP | ||||||
![]() | Orotidine-5'-phosphate decarboxylase | ||||||
![]() | LYASE / decarboxylase / tim barrel / unusual catalysis / Disease mutation / Glycosyltransferase / Multifunctional enzyme / 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 | ![]() ![]() ![]() | ||||||
![]() | Heinrich, D. / Diederichsen, U. / Rudolph, M. | ||||||
![]() | ![]() Title: Lys314 is a nucleophile in non-classical reactions of orotidine-5'-monophosphate decarboxylase Authors: Heinrich, D. / Diederichsen, U. / Rudolph, M.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 122.5 KB | Display | ![]() |
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PDB format | ![]() | 94.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 25.8 KB | Display | |
Data in CIF | ![]() | 37.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ewuC ![]() 3ewwC ![]() 3ewxC ![]() 3ewyC ![]() 3ewzC ![]() 3ex2C ![]() 3ex3C ![]() 3ex4C ![]() 3ex6C ![]() 3l0kC ![]() 3l0nC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 28299.742 Da / Num. of mol.: 2 / Fragment: UNP residues 224-480 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P11172, orotidine-5'-phosphate decarboxylase #2: Chemical | ChemComp-U5P / | #3: Chemical | ChemComp-GOL / | #4: Chemical | ChemComp-6CN / | #5: Water | ChemComp-HOH / | Nonpolymer details | ACCORDING TO AUTHORS, THE LIGAND 6CN HAS DISTORTED GEOMETRY WHEN IN COMPLEX WITH THE ENZYME. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.82 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1 M Tris-HCl pH 8.0, 1.8 M (NH4)2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 300.0K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 29, 2008 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.4→42.5 Å / Num. obs: 107488 / % possible obs: 99.8 % / Redundancy: 3.6 % / Rsym value: 0.074 / Net I/σ(I): 7.9 | |||||||||||||||
Reflection shell | Resolution: 1.4→1.44 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.4 / Num. unique all: 6504 / Rsym value: 0.602 / % possible all: 98.5 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.918 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→38.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20 /
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