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Yorodumi- PDB-1six: Mycobacterium tuberculosis dUTPase complexed with magnesium and a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1six | ||||||
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Title | Mycobacterium tuberculosis dUTPase complexed with magnesium and alpha,beta-imido-dUTP | ||||||
Components | Deoxyuridine 5'-triphosphate nucleotidohydrolase | ||||||
Keywords | HYDROLASE / jelly-roll / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC | ||||||
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 / Resolution: 1.3 Å | ||||||
Authors | Sawaya, M.R. / Chan, S. / Segelke, B. / Lekin, T. / Krupka, H. / Cho, U.-S. / Kim, M. / So, M. / Kim, C.-Y. / Naranjo, C.M. ...Sawaya, M.R. / Chan, S. / Segelke, B. / Lekin, T. / Krupka, H. / Cho, U.-S. / Kim, M. / So, M. / Kim, C.-Y. / Naranjo, C.M. / Rogers, Y.C. / Park, M.S. / Waldo, G.S. / Pashkov, I. / Cascio, D. / Yeates, T.O. / Perry, J.L. / Terwilliger, T.C. / Eisenberg, D. / TB Structural Genomics Consortium (TBSGC) | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: Crystal structure of the Mycobacterium tuberculosis dUTPase: insights into the catalytic mechanism. Authors: Chan, S. / Segelke, B. / Lekin, T. / Krupka, H. / Cho, U.S. / Kim, M.-Y. / So, M. / Kim, C.-Y. / Naranjo, C.M. / Rogers, Y.C. / Park, M.S. / Waldo, G.S. / Pashkov, I. / Cascio, D. / Perry, J.L. / Sawaya, M.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1six.cif.gz | 80.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1six.ent.gz | 57.3 KB | Display | PDB format |
PDBx/mmJSON format | 1six.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1six_validation.pdf.gz | 800.9 KB | Display | wwPDB validaton report |
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Full document | 1six_full_validation.pdf.gz | 803.1 KB | Display | |
Data in XML | 1six_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | 1six_validation.cif.gz | 13.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/si/1six ftp://data.pdbj.org/pub/pdb/validation_reports/si/1six | HTTPS FTP |
-Related structure data
Related structure data | 1mq7SC 1sjnC 1slhC 1sm8C 1smcC 1snfC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-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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Details | The second and third part of the biological assembly is generated by the three-fold axis: -Y+1,X-Y,Z and Y-X+1,-X+1,Z |
-Components
#1: Protein | Mass: 17992.314 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: DUT, RV2697C, MT2771, MTCY05A6.18C, MB2716C / Plasmid: modified pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21PRO References: UniProt: P0A552, UniProt: P9WNS5*PLUS, dUTP diphosphatase |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-DUP / |
#4: Chemical | ChemComp-TRS / |
#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: 1.69 Å3/Da / Density % sol: 27.3 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 3350, magnesium nitrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9786 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 12, 2003 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→90 Å / Num. all: 35121 / Num. obs: 35121 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.1 % / Biso Wilson estimate: 15.5 Å2 / Rsym value: 0.125 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 1.3→1.35 Å / Redundancy: 8.2 % / Mean I/σ(I) obs: 7.3 / Num. unique all: 3466 / Rsym value: 0.319 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1MQ7 Resolution: 1.3→20 Å / Num. parameters: 11371 / Num. restraintsaints: 13957 / Isotropic thermal model: anisotropic / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER Details: The crystal was refined in SHELX using a merohedral twin operator TWIN 0 1 0 1 0 0 0 0 -1 (equivalently expressed as k,h,-l) twin fraction =0.163.
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.6 Å2 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1258.96 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→20 Å
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Refine LS restraints |
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