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- PDB-3ex4: human orotidyl-5'-monophosphate decarboxylase in complex with BMP -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ex4 | ||||||
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Title | human orotidyl-5'-monophosphate decarboxylase in complex with BMP | ||||||
![]() | Orotidine-5'-phosphate decarboxylase![]() | ||||||
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Function / homology | ![]() UMP biosynthetic process / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() 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 | ![]() | 129.7 KB | Display | ![]() |
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PDB format | ![]() | 100.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3ewuC ![]() 3ewwC ![]() 3ewxC ![]() 3ewyC ![]() 3ewzC ![]() 3ex1C ![]() 3ex2C ![]() 3ex3C ![]() 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | ![]() Mass: 28299.742 Da / Num. of mol.: 1 / Fragment: UNP residues 224-480 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P11172, ![]() |
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#2: Chemical | ChemComp-BMP / |
#3: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.36 % |
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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: May 24, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.24→44.7 Å / Num. obs: 78072 / % possible obs: 98.9 % / Redundancy: 6.1 % / Rsym value: 0.075 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.24→1.26 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 517 / Rsym value: 0.359 / % possible all: 47.1 |
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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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.62 Å2
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Refinement step | Cycle: LAST / Resolution: 1.24→38.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.24→1.28 Å / Total num. of bins used: 20
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