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Yorodumi- PDB-2zz7: Orotidine Monophosphate Decarboxylase K72A mutant complexed with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zz7 | ||||||
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Title | Orotidine Monophosphate Decarboxylase K72A mutant complexed with BMP (produced from 6-Iodo-UMP) | ||||||
Components | Orotidine 5'-phosphate decarboxylase | ||||||
Keywords | LYASE / ODCase / OMPDC / OMPDCase / Decarboxylase / Pyrimidine biosynthesis | ||||||
Function / homology | Function and homology information 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 | Methanothermobacter thermautotrophicus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.58 Å | ||||||
Authors | Fujihashi, M. / Pai, E.F. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zz7.cif.gz | 63.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zz7.ent.gz | 46.5 KB | Display | PDB format |
PDBx/mmJSON format | 2zz7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zz7_validation.pdf.gz | 770.2 KB | Display | wwPDB validaton report |
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Full document | 2zz7_full_validation.pdf.gz | 771.7 KB | Display | |
Data in XML | 2zz7_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | 2zz7_validation.cif.gz | 18.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zz/2zz7 ftp://data.pdbj.org/pub/pdb/validation_reports/zz/2zz7 | HTTPS FTP |
-Related structure data
Related structure data | 2zz1C 2zz2C 2zz3C 2zz4C 2zz5C 2zz6C C: citing same article (ref.) |
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Similar structure data |
-Links
-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: 27321.299 Da / Num. of mol.: 1 / Mutation: K72A,R226L,I227N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea) Plasmid: pET-15b / Production host: Escherichia coli (E. coli) References: UniProt: O26232, orotidine-5'-phosphate decarboxylase | ||||
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#2: Chemical | ChemComp-BMP / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | ACCORDING TO DEPOSITORS, PRO101 IS CORRECT AND UNIPORT IS PROBABLY INCORRECT AT THIS POSITION. ...ACCORDING TO DEPOSITORS | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.9 % |
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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: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1.0332 Å |
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Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 6, 2004 / Details: default |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→200 Å / Num. obs: 30641 / % possible obs: 99.9 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 33.2 |
Reflection shell | Resolution: 1.58→1.61 Å / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: ODCase from M. thermoautotrophicum Resolution: 1.58→51.64 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.224 / SU ML: 0.041 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.881 Å2
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Refinement step | Cycle: LAST / Resolution: 1.58→51.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.58→1.621 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 18.7778 Å / Origin y: 40.3435 Å / Origin z: 29.5132 Å
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Refinement TLS group |
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