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Yorodumi- PDB-2zz6: Covalent complex of orotidine monophosphate decarboxylase from M.... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zz6 | ||||||
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Title | Covalent complex of orotidine monophosphate decarboxylase from M. thermoautotrophicum with 6-azido-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: 1.66 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 | 2zz6.cif.gz | 106.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zz6.ent.gz | 80.6 KB | Display | PDB format |
PDBx/mmJSON format | 2zz6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zz6_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 2zz6_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 2zz6_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | 2zz6_validation.cif.gz | 30.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zz/2zz6 ftp://data.pdbj.org/pub/pdb/validation_reports/zz/2zz6 | HTTPS FTP |
-Related structure data
Related structure data | 2zz1C 2zz2C 2zz3C 2zz4C 2zz5C 2zz7C 1x1zS S: Starting model for refinement 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
#1: Protein | Mass: 27379.402 Da / Num. of mol.: 2 / Mutation: R226L,I227N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea) Plasmid: pET15b / Production host: Escherichia coli (E. coli) References: UniProt: O26232, orotidine-5'-phosphate decarboxylase #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | Nonpolymer details | THIS COMPLEX WAS PREPARED BY ENZYME AND 6-AZIDO-UMP. THE AZIDO GROUP WAS REPLACED BY THE AMINO ...THIS COMPLEX WAS PREPARED BY ENZYME AND 6-AZIDO-UMP. THE AZIDO 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.82 % |
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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-BM-D / Wavelength: 0.9795 Å |
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Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 5, 2004 / Details: default |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→100 Å / Num. obs: 50234 / % possible obs: 98.3 % / Redundancy: 3.8 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 1.66→1.69 Å / Mean I/σ(I) obs: 4.5 / Rsym value: 0.31 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1X1Z Resolution: 1.66→27.44 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1275687.77 / 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: 44.5725 Å2 / ksol: 0.413001 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.66→27.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.66→1.72 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 10
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Xplor file |
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