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- PDB-3gdr: Crystal structure of the D91N mutant of the orotidine 5'-monophos... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3gdr | ||||||
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Title | Crystal structure of the D91N mutant of the orotidine 5'-monophosphate decarboxylase from Saccharomyces cerevisiae | ||||||
![]() | Orotidine 5'-phosphate decarboxylase | ||||||
![]() | LYASE / orotidine 5'-monophosphate decarboxylase / Saccharomyces cerevisiae / D91N mutant / Decarboxylase / Phosphoprotein / Pyrimidine biosynthesis / Ubl conjugation | ||||||
Function / homology | ![]() UMP biosynthetic process / orotate phosphoribosyltransferase activity / orotidine-5'-phosphate decarboxylase / orotidine-5'-phosphate decarboxylase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fedorov, A.A. / Fedorov, E.V. / Wood, B.M. / Gerlt, J.A. / Almo, S.C. | ||||||
![]() | ![]() Title: Mechanism of the orotidine 5'-monophosphate decarboxylase-catalyzed reaction: evidence for substrate destabilization. Authors: Chan, K.K. / Wood, B.M. / Fedorov, A.A. / Fedorov, E.V. / Imker, H.J. / Amyes, T.L. / Richard, J.P. / Almo, S.C. / Gerlt, J.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 206.1 KB | Display | ![]() |
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PDB format | ![]() | 167.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 454.2 KB | Display | ![]() |
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Full document | ![]() | 463.4 KB | Display | |
Data in XML | ![]() | 41.3 KB | Display | |
Data in CIF | ![]() | 58.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3g18C ![]() 3g1aC ![]() 3g1dC ![]() 3g1fC ![]() 3g1hC ![]() 3g1sC ![]() 3g1vC ![]() 3g1xC ![]() 3g1yC ![]() 3g22C ![]() 3g24C ![]() 3gdkSC ![]() 3gdlC ![]() 3gdtC S: Starting model for refinement 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 29278.547 Da / Num. of mol.: 4 / Mutation: D91N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: URA3, YEL021W / Production host: ![]() ![]() References: UniProt: P03962, orotidine-5'-phosphate decarboxylase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 25% PEG 3350, 0.1M Bis-Tris, 0.2M Sodium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 19, 2007 |
Radiation | Monochromator: Si(111) CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→25 Å / Num. all: 83436 / Num. obs: 83436 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.074 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3GDK Resolution: 1.9→24.86 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1828484.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.6847 Å2 / ksol: 0.379566 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→24.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.97 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 10
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Xplor file |
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