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Yorodumi- PDB-3v75: Crystal structure of putative orotidine 5'-phosphate decarboxylas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3v75 | |||||||||
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Title | Crystal structure of putative orotidine 5'-phosphate decarboxylase from Streptomyces avermitilis ma-4680 | |||||||||
Components | Orotidine 5'-phosphate decarboxylase | |||||||||
Keywords | LYASE / STRUCTURAL GENOMICS / PSI-2 / PROTEIN STRUCTURE INITIATIVE / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG / TIM BARREL / 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 Similarity search - Function | |||||||||
Biological species | Streptomyces avermitilis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å | |||||||||
Authors | Stogios, P.J. / Xu, X. / Cui, H. / Kudritska, M. / Tan, K. / Edwards, A. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | |||||||||
Citation | Journal: To be Published Title: Crystal structure of putative orotidine 5'-phosphate decarboxylase from Streptomyces avermitilis ma-4680 Authors: Stogios, P.J. / Xu, X. / Cui, H. / Kudritska, M. / Tan, K. / Edwards, A. / Savchenko, A. / Joachimiak, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3v75.cif.gz | 131.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3v75.ent.gz | 107.8 KB | Display | PDB format |
PDBx/mmJSON format | 3v75.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v7/3v75 ftp://data.pdbj.org/pub/pdb/validation_reports/v7/3v75 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-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: 31675.654 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces avermitilis (bacteria) / Strain: MA-4680 / Gene: pyrF, SAV6869, SAV_6869 / Plasmid: P15TV-L / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: Q827Q5, orotidine-5'-phosphate decarboxylase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.84 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M TRIS PH 8.5, 0.2 M SODIUM ACETATE, 30% PEG 4K, TEV PROTEASE, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97915 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 24, 2009 / Details: MIRRORS |
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: 1.35→50 Å / Num. all: 57832 / Num. obs: 53899 / % possible obs: 93.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Rsym value: 0.063 / Net I/σ(I): 43.24 |
Reflection shell | Resolution: 1.35→1.37 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3.79 / Rsym value: 0.392 / % possible all: 61 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.4→27.444 Å / SU ML: 0.17 / σ(F): 0.12 / Phase error: 15.95 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.287 Å2 / ksol: 0.379 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.4→27.444 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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