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Yorodumi- PDB-1mq7: CRYSTAL STRUCTURE OF DUTPASE FROM MYCOBACTERIUM TUBERCULOSIS (RV2697C) -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mq7 | ||||||
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Title | CRYSTAL STRUCTURE OF DUTPASE FROM MYCOBACTERIUM TUBERCULOSIS (RV2697C) | ||||||
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: 1.95 Å | ||||||
Authors | Sawaya, M.R. / Chan, S. / Segelke, B.W. / Lekin, T. / Heike, K. / Cho, U.S. / Naranjo, C. / Perry, L.J. / Yeates, T.O. / 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. #1: Journal: STRUCTURE / Year: 1996 Title: HUMAN DUTP PYROPHOSPHATASE: URACIL RECOGNITION BY A BETA HAIRPIN AND ACTIVE SITES FORMED BY THREE SEPARATE SUBUNITS Authors: Mol, C.D. / Harris, J.M. / Mclntosh, E.M. / Tainer, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mq7.cif.gz | 41 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mq7.ent.gz | 28.2 KB | Display | PDB format |
PDBx/mmJSON format | 1mq7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mq7_validation.pdf.gz | 435.9 KB | Display | wwPDB validaton report |
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Full document | 1mq7_full_validation.pdf.gz | 436.8 KB | Display | |
Data in XML | 1mq7_validation.xml.gz | 9.2 KB | Display | |
Data in CIF | 1mq7_validation.cif.gz | 12.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mq/1mq7 ftp://data.pdbj.org/pub/pdb/validation_reports/mq/1mq7 | HTTPS FTP |
-Related structure data
Related structure data | 1sixC 1sjnC 1slhC 1sm8C 1smcC 1snfC 1dudS 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 biological assembly is a trimer that is generated by the following crystallographic symmetry operators -y+1, -z+1, x and z, -x+1, -y+1 |
-Components
#1: Protein | Mass: 15820.938 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: Rv2697c / Production host: Escherichia coli (E. coli) References: UniProt: P0A552, UniProt: P9WNS5*PLUS, dUTP diphosphatase | ||
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#2: Chemical | #3: 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: 2.54 Å3/Da / Density % sol: 51.58 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG4000, EDTA, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 23, 2002 |
Radiation | Monochromator: Si (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→31.25 Å / Num. all: 11317 / Num. obs: 11317 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 18 % / Biso Wilson estimate: 17.3 Å2 / Rsym value: 0.078 / Net I/σ(I): 62.7 |
Reflection shell | Resolution: 1.95→2.02 Å / Num. unique all: 1172 / Rsym value: 0.393 / % possible all: 100 |
Reflection | *PLUS Num. obs: 11592 / Num. measured all: 208809 / Rmerge(I) obs: 0.078 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 13.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DUD Resolution: 1.95→31.25 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.1896 Å2 / ksol: 0.366749 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.8 Å2
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Refine analyze | Luzzati coordinate error free: 0.26 Å / Luzzati sigma a free: 0.14 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→31.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.07 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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