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- PDB-3l0n: Human orotidyl-5'-monophosphate decarboxylase in complex with 6-m... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3l0n | |||||||||
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Title | Human orotidyl-5'-monophosphate decarboxylase in complex with 6-mercapto-UMP | |||||||||
![]() | Uridine 5'-monophosphate synthase | |||||||||
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Function / homology | ![]() UMP biosynthetic process / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Heinrich, D. / Wittmann, J. / 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 | ![]() | 114.6 KB | Display | ![]() |
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PDB format | ![]() | 88.3 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 ![]() 3ex4C ![]() 3ex6C ![]() 3l0kC 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, ![]() #2: Chemical | #3: Water | ChemComp-HOH / | ![]() Nonpolymer details | ACCORDING TO AUTHORS, THE LIGAND S5P HAS DISTORTED GEOMETRY UPON BINDING TO THE PROTEIN. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.67 % |
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Crystal grow![]() | Temperature: 300 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1M Tris-HCl pH 8.0, 1.8M (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: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 29, 2007 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength![]() | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.74→34.65 Å / Num. obs: 53875 / % possible obs: 97.6 % / Redundancy: 4.9 % / Biso Wilson estimate: 26.463 Å2 / Rsym value: 0.078 / Net I/σ(I): 12.6 | |||||||||||||||
Reflection shell | Resolution: 1.75→1.79 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 1.4 / Num. unique all: 2192 / Rsym value: 0.575 / % possible all: 80 |
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Processing
Software | Name: REFMAC / Version: 5.6.0041 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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: 22.011 Å2
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Refinement step | Cycle: LAST / Resolution: 1.74→34.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.742→1.787 Å / Total num. of bins used: 20
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