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Yorodumi- PDB-4mjz: 2.75 Angstrom Resolution Crystal Structure of Putative Orotidine-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4mjz | ||||||
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Title | 2.75 Angstrom Resolution Crystal Structure of Putative Orotidine-monophosphate-decarboxylase from Toxoplasma gondii. | ||||||
Components | Orotidine 5'-phosphate decarboxylase | ||||||
Keywords | LYASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | Function and homology information orotidine-5'-phosphate decarboxylase / orotidine-5'-phosphate decarboxylase activity / glycosyltransferase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process Similarity search - Function | ||||||
Biological species | Toxoplasma gondii (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Minasov, G. / Wawrzak, Z. / Ruan, J. / Ngo, H. / Shuvalova, L. / Dubrovska, I. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: TO BE PUBLISHED Title: 2.75 Angstrom Resolution Crystal Structure of Putative Orotidine-monophosphate-decarboxylase from Toxoplasma gondii. Authors: Minasov, G. / Wawrzak, Z. / Ruan, J. / Ngo, H. / Shuvalova, L. / Dubrovska, I. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mjz.cif.gz | 233.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mjz.ent.gz | 189.8 KB | Display | PDB format |
PDBx/mmJSON format | 4mjz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4mjz_validation.pdf.gz | 473.5 KB | Display | wwPDB validaton report |
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Full document | 4mjz_full_validation.pdf.gz | 485 KB | Display | |
Data in XML | 4mjz_validation.xml.gz | 23.6 KB | Display | |
Data in CIF | 4mjz_validation.cif.gz | 32 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mj/4mjz ftp://data.pdbj.org/pub/pdb/validation_reports/mj/4mjz | HTTPS FTP |
-Related structure data
Related structure data | 3qw4S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 35041.387 Da / Num. of mol.: 2 / Fragment: UNP residues 12-318 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Strain: ME49 / Gene: TGGT1_010340 / Plasmid: pCCK-N'-6XHisTag-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic References: UniProt: B9PKU1, UniProt: B6KBH9*PLUS, orotidine-5'-phosphate decarboxylase #2: Chemical | ChemComp-PEG / #3: Chemical | ChemComp-PGE / | #4: Chemical | ChemComp-NO3 / | #5: Water | ChemComp-HOH / | |
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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: 2.09 Å3/Da / Density % sol: 41.09 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.3 Details: Protein: 7.7 mG/mL, 0.5 M Sodium chloride, 0.01 M Tris-HCL buffer pH 8.3, 0.02M Magnesium chloride, 0.02M UMP Screen: JCSG+(C3), 0.2M Ammonium nitrate pH 6.3, 20% (w/v) PEG 3350, VAPOR ...Details: Protein: 7.7 mG/mL, 0.5 M Sodium chloride, 0.01 M Tris-HCL buffer pH 8.3, 0.02M Magnesium chloride, 0.02M UMP Screen: JCSG+(C3), 0.2M Ammonium nitrate pH 6.3, 20% (w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 20, 2013 / Details: Beryllium lenses |
Radiation | Monochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→30 Å / Num. all: 16220 / Num. obs: 16220 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 14.1 % / Biso Wilson estimate: 53.3 Å2 / Rmerge(I) obs: 0.124 / Net I/σ(I): 24.2 |
Reflection shell | Resolution: 2.75→2.8 Å / Redundancy: 14.3 % / Rmerge(I) obs: 0.591 / Mean I/σ(I) obs: 5.3 / Num. unique all: 797 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3QW4 Resolution: 2.75→29.1 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.906 / SU B: 27.675 / SU ML: 0.265 Isotropic thermal model: Thermal Factors Individually Refined Cross valid method: THROUGHOUT / ESU R Free: 0.374 / 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: 46.175 Å2
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Refinement step | Cycle: LAST / Resolution: 2.75→29.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.75→2.821 Å / Total num. of bins used: 20
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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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