+Open data
-Basic information
Entry | Database: PDB / ID: 3hza | ||||||
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Title | Crystal structure of dUTPase H145W mutant | ||||||
Components | Deoxyuridine 5'-triphosphate nucleotidohydrolase | ||||||
Keywords | HYDROLASE / jelly roll / domain swapping / 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 / FOURIER SYNTHESIS / Resolution: 1.2 Å | ||||||
Authors | Leveles, I. / Harmat, V. / Pecsi, I. / Toth, J. / Vertessy, B.G. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2010 Title: Aromatic stacking between nucleobase and enzyme promotes phosphate ester hydrolysis in dUTPase. Authors: Pecsi, I. / Leveles, I. / Harmat, V. / Vertessy, B.G. / Toth, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hza.cif.gz | 90.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hza.ent.gz | 65.9 KB | Display | PDB format |
PDBx/mmJSON format | 3hza.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3hza_validation.pdf.gz | 802.2 KB | Display | wwPDB validaton report |
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Full document | 3hza_full_validation.pdf.gz | 803.7 KB | Display | |
Data in XML | 3hza_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | 3hza_validation.cif.gz | 16.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hz/3hza ftp://data.pdbj.org/pub/pdb/validation_reports/hz/3hza | HTTPS FTP |
-Related structure data
Related structure data | 3lojC 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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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 18040.377 Da / Num. of mol.: 1 / Mutation: H145W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: dut, Rv2697c, MT2771, MTCY05A6.18c / 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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-Non-polymers , 5 types, 201 molecules
#2: Chemical | ChemComp-MG / | ||||
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#3: Chemical | ChemComp-DUP / | ||||
#4: Chemical | #5: Chemical | ChemComp-TRS / | #6: 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: 2.03 Å3/Da / Density % sol: 39.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.3 M Ammonium sulfate, 50 mM Tris-HCl, 12 % Glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.97861 Å |
Detector | Type: MARMOSAIC 325 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: 1.2→20 Å / Num. obs: 42370 / % possible obs: 94.2 % / Observed criterion σ(I): -3 / Redundancy: 3.73 % / Biso Wilson estimate: 16.422 Å2 / Rsym value: 0.039 / Net I/σ(I): 18.4 |
Reflection shell | Resolution: 1.2→1.23 Å / Redundancy: 1.467 % / Mean I/σ(I) obs: 2.02 / Num. unique all: 2286 / Rsym value: 0.472 / % possible all: 68.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 2PY4 Resolution: 1.2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: 1. Used CGLS procedure. 2. Atomic anisotropic B values were refined for non-hydrogen atoms. 3. Hydrogen atoms were generated in the riding positions.
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Refinement step | Cycle: LAST / Resolution: 1.2→20 Å
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Refine LS restraints |
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