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- PDB-2zz3: Covalent complex of orotidine monophosphate decarboxylase D70A mu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2zz3 | ||||||
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Title | Covalent complex of orotidine monophosphate decarboxylase D70A mutant from M. thermoautotrophicus with 6-cyano-UMP | ||||||
![]() | Orotidine 5'-phosphate decarboxylase | ||||||
![]() | LYASE / ODCase / OMPDCase / OMPDC / Decarboxylase / Pyrimidine biosynthesis | ||||||
Function / homology | ![]() 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 | ![]() ![]() ![]() | ||||||
![]() | Fujihashi, M. / Pai, E.F. | ||||||
![]() | ![]() Title: Structural characterization of the molecular events during a slow substrate-product transition in orotidine 5'-monophosphate decarboxylase Authors: Fujihashi, M. / Wei, L. / Kotra, L.P. / Pai, E.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 105.4 KB | Display | ![]() |
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PDB format | ![]() | 79.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 20.9 KB | Display | |
Data in CIF | ![]() | 29.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2zz1C ![]() 2zz2C ![]() 2zz4C ![]() 2zz5C ![]() 2zz6C ![]() 2zz7C ![]() 1x1zS 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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Unit cell |
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Components
#1: Protein | Mass: 27335.391 Da / Num. of mol.: 2 / Mutation: D70A,R226L,I227N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: pET15b / Production host: ![]() ![]() References: UniProt: O26232, orotidine-5'-phosphate decarboxylase #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | Nonpolymer details | THIS COMPLEX WAS PREPARED BY MIXING D70A MUTANT ENZYME AND 6-CYANO-UMP. THE CN GROUP WAS REPLACED ...THIS COMPLEX WAS PREPARED BY MIXING D70A MUTANT ENZYME AND 6-CYANO-UMP. THE CN GROUP WAS REPLACED BY THE AMINO GROUP OF LYS 72. | Sequence details | ACCORDING TO DEPOSITORS, PRO101 IS CORRECT AND UNIPORT IS PROBABLY INCORRECT AT THIS POSITION. ...ACCORDING TO DEPOSITORS | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.08 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion Details: 1.2-1.36M Sodium Citrate, 5% dioxiane, pH 6.0-8.5, VAPOR DIFFUSION, temperature 298K PH range: 6.0-8.5 |
-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
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Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 7, 2004 / Details: default |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.127 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→100 Å / Num. obs: 38640 / % possible obs: 87.9 % / Redundancy: 3.62 % / Biso Wilson estimate: 13.6 Å2 / Rsym value: 0.063 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 1.8→1.83 Å / Mean I/σ(I) obs: 3 / Rsym value: 0.273 / % possible all: 57 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1x1z Resolution: 1.8→22.19 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1322201.97 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 47.1215 Å2 / ksol: 0.419454 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→22.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.86 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 10
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Xplor file |
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