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Yorodumi- PDB-5edd: Crystal structure of Mycobacterium tuberculosis dUTPase R140K, H1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5edd | ||||||||||||
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Title | Crystal structure of Mycobacterium tuberculosis dUTPase R140K, H145W mutant | ||||||||||||
Components | Deoxyuridine 5'-triphosphate nucleotidohydrolase | ||||||||||||
Keywords | HYDROLASE / JELLY-ROLL / ENZYME-LIGAND COMPLEX | ||||||||||||
Function / homology | Function and homology information dUTP metabolic process / dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / magnesium ion binding Similarity search - Function | ||||||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.97 Å | ||||||||||||
Authors | Nagy, G.N. / Leveles, I. / Lopata, A. / Harmat, V. / Toth, J. / Vertessy, G.B. | ||||||||||||
Funding support | Hungary, 3items
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Citation | Journal: J. Am. Chem. Soc. / Year: 2016 Title: Structural Characterization of Arginine Fingers: Identification of an Arginine Finger for the Pyrophosphatase dUTPases. Authors: Nagy, G.N. / Suardiaz, R. / Lopata, A. / Ozohanics, O. / Vekey, K. / Brooks, B.R. / Leveles, I. / Toth, J. / Vertessy, B.G. / Rosta, E. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5edd.cif.gz | 72.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5edd.ent.gz | 51.5 KB | Display | PDB format |
PDBx/mmJSON format | 5edd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5edd_validation.pdf.gz | 794.4 KB | Display | wwPDB validaton report |
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Full document | 5edd_full_validation.pdf.gz | 794.5 KB | Display | |
Data in XML | 5edd_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | 5edd_validation.cif.gz | 13.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ed/5edd ftp://data.pdbj.org/pub/pdb/validation_reports/ed/5edd | HTTPS FTP |
-Related structure data
Related structure data | 5ectC 3hzaS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 18012.363 Da / Num. of mol.: 1 / Mutation: R140K,H145W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: dut, MRA_2725 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A5U649, UniProt: P9WNS5*PLUS, dUTP diphosphatase |
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#2: Chemical | ChemComp-TRS / |
#3: Chemical | ChemComp-DUP / |
#4: Chemical | ChemComp-MG / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 1.5 M ammonium sulfate, 0.1M Tris/HCl, 12% glycerol, 6.7 mM dUPnPP, 20 mM magnesium chloride PH range: 7.5-8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SEALED TUBE / Type: OTHER / Wavelength: 1.54056 Å |
Detector | Type: AGILENT EOS CCD / Detector: CCD / Date: Sep 18, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54056 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→41.91 Å / Num. all: 10220 / Num. obs: 10220 / % possible obs: 99.8 % / Redundancy: 3.51 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 1.97→2.08 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 1.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3HZA Resolution: 1.97→41.91 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.931 / SU B: 8.32 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.15 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.018 Å2
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Refinement step | Cycle: LAST / Resolution: 1.97→41.91 Å
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Refine LS restraints |
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