+Open data
-Basic information
Entry | Database: PDB / ID: 3h6d | ||||||
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Title | Structure of the mycobacterium tuberculosis DUTPase D28N mutant | ||||||
Components | Deoxyuridine 5'-triphosphate nucleotidohydrolase | ||||||
Keywords | HYDROLASE / jelly-roll / Nucleotide metabolism | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å | ||||||
Authors | Leveles, I. / Harmat, V. / Nagy, G. / Takacs, E. / Lopata, A. / Toth, J. / Vertessy, B.G. | ||||||
Citation | Journal: Febs Lett. / Year: 2010 Title: Direct contacts between conserved motifs of different subunits provide major contribution to active site organization in human and mycobacterial dUTPases. Authors: Takacs, E. / Nagy, G. / Leveles, I. / Harmat, V. / Lopata, A. / Toth, J. / Vertessy, B.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3h6d.cif.gz | 47.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3h6d.ent.gz | 31.2 KB | Display | PDB format |
PDBx/mmJSON format | 3h6d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3h6d_validation.pdf.gz | 819.1 KB | Display | wwPDB validaton report |
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Full document | 3h6d_full_validation.pdf.gz | 819.6 KB | Display | |
Data in XML | 3h6d_validation.xml.gz | 9.2 KB | Display | |
Data in CIF | 3h6d_validation.cif.gz | 12.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h6/3h6d ftp://data.pdbj.org/pub/pdb/validation_reports/h6/3h6d | HTTPS FTP |
-Related structure data
Related structure data | 3i93C 2py4S 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 17991.330 Da / Num. of mol.: 1 / Mutation: D28N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: dut, MT2771, MTCY05A6.18c, Rv2697c / Plasmid: PET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) References: UniProt: P0A552, UniProt: P9WNS5*PLUS, dUTP diphosphatase | ||
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#2: Chemical | ChemComp-MG / | ||
#3: Chemical | ChemComp-DUP / | ||
#4: Chemical | #5: 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: 2.05 Å3/Da / Density % sol: 39.91 % |
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Crystal grow | Temperature: 298 K / pH: 8.5 Details: 1.45 M Ammonium sulphate, 50 mM Tris, 12% Glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.97861 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 12, 2008 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL SI[111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97861 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 13348 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.39 % / Biso Wilson estimate: 26.12 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 14.58 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 2.54 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 2.41 / % possible all: 99.2 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2PY4 Resolution: 1.8→19.16 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.941 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 5.508 / SU ML: 0.077 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ARG 140 WAS ASSIGNED TO ELECTRON DENSITY BASED ON STRUCTURAL ALIGNMENT TO THE NATIVE ENZYME.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.224 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→19.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.846 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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