+Open data
-Basic information
Entry | Database: PDB / ID: 4gcy | ||||||
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Title | Structure of Mycobacterium tuberculosis dUTPase H21W mutant | ||||||
Components | Deoxyuridine 5'-triphosphate nucleotidohydrolase | ||||||
Keywords | HYDROLASE / jelly-roll | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Toth, J. / Vertessy, B.G. / Leveles, I. / Bendes, A. | ||||||
Citation | Journal: To be Published Title: RAMD identification of substrate binding pathways to the active site of dUTPase Authors: Toth, J. / Vertessy, B.G. / Leveles, I. / Bendes, A. / Lopata, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gcy.cif.gz | 84.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gcy.ent.gz | 63.2 KB | Display | PDB format |
PDBx/mmJSON format | 4gcy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4gcy_validation.pdf.gz | 820.9 KB | Display | wwPDB validaton report |
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Full document | 4gcy_full_validation.pdf.gz | 823.1 KB | Display | |
Data in XML | 4gcy_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | 4gcy_validation.cif.gz | 15.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gc/4gcy ftp://data.pdbj.org/pub/pdb/validation_reports/gc/4gcy | HTTPS FTP |
-Related structure data
Related structure data | |
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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: H21W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: dut, Rv2697c, MT2771, MTCY05A6.18c / 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, 160 molecules
#2: Chemical | ChemComp-DUP / |
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#3: Chemical | ChemComp-TRS / |
#4: Chemical | ChemComp-MG / |
#5: Chemical | ChemComp-GOL / |
#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: 39.26 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.5M ammonium sulphate, 0.1M Tris/HCl, 10% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 6, 2010 / Details: Blue Confocal Max-Flux optics |
Radiation | Monochromator: confocal mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→27.95 Å / Num. all: 23022 / Num. obs: 23022 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3346 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→27.47 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.973 / SU B: 2.472 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.062 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.815 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→27.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 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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