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Yorodumi- PDB-3wjw: Wild-type orotidine 5'-monophosphate decarboxylase from M. thermo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wjw | ||||||
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Title | Wild-type orotidine 5'-monophosphate decarboxylase from M. thermoautotrophicus complexed with 6-methyl-UMP | ||||||
Components | Orotidine 5'-phosphate decarboxylase | ||||||
Keywords | LYASE / TIM barrel / Decarboxylase / pyrimidine biosynthesis / protein-ligand complex | ||||||
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: 1.59 Å | ||||||
Authors | Fujihashi, M. / Kuroda, S. / Pai, E.F. / Miki, K. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2013 Title: Substrate distortion contributes to the catalysis of orotidine 5'-monophosphate decarboxylase. Authors: Fujihashi, M. / Ishida, T. / Kuroda, S. / Kotra, L.P. / Pai, E.F. / Miki, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wjw.cif.gz | 104.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wjw.ent.gz | 79.8 KB | Display | PDB format |
PDBx/mmJSON format | 3wjw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3wjw_validation.pdf.gz | 752.5 KB | Display | wwPDB validaton report |
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Full document | 3wjw_full_validation.pdf.gz | 753.2 KB | Display | |
Data in XML | 3wjw_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | 3wjw_validation.cif.gz | 16.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wj/3wjw ftp://data.pdbj.org/pub/pdb/validation_reports/wj/3wjw | HTTPS FTP |
-Related structure data
Related structure data | 3wjxC 3wjySC 3wjzC 3wk0C 3wk1C 3wk2C 3wk3C C: citing same article (ref.) S: Starting model for refinement |
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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: 27379.402 Da / Num. of mol.: 1 / Mutation: L226R, N227I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea) Strain: ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H Gene: pyrF, MTH_129 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) References: UniProt: O26232, orotidine-5'-phosphate decarboxylase |
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#2: Chemical | ChemComp-U6M / |
#3: 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: 2.02 Å3/Da / Density % sol: 39.01 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6 Details: Sodium citrate, pH 6, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→51.78 Å / Num. obs: 30174 / % possible obs: 100 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 29.5 |
Reflection shell | Resolution: 1.59→1.63 Å / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 6.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3WJY Resolution: 1.59→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.959 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 2.525 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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 max: 57.58 Å2 / Biso mean: 19.1653 Å2 / Biso min: 7.89 Å2
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Refinement step | Cycle: LAST / Resolution: 1.59→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.59→1.631 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 18.6002 Å / Origin y: 40.5617 Å / Origin z: 29.7071 Å
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Refinement TLS group |
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