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Yorodumi- PDB-1sjn: Mycobacterium tuberculosis dUTPase complexed with magnesium and a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1sjn | ||||||
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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: 1.8 Å | ||||||
Authors | Sawaya, M.R. / Chan, S. / Segelke, B. / Lekin, T. / Krupka, H. / Cho, U.S. / Kim, M.-Y. / So, M. / Kim, C.-Y. / Naranjo, C.M. ...Sawaya, M.R. / 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. / 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 | 1sjn.cif.gz | 101 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1sjn.ent.gz | 75 KB | Display | PDB format |
PDBx/mmJSON format | 1sjn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1sjn_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 1sjn_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 1sjn_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | 1sjn_validation.cif.gz | 28.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sj/1sjn ftp://data.pdbj.org/pub/pdb/validation_reports/sj/1sjn | HTTPS FTP |
-Related structure data
Related structure data | 1mq7C 1sixSC 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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Details | The biological assembly is a homotrimer. It is contained within the asymmetric unit. |
-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 17572.871 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: DUT, RV2697C, MT2771, MTCY05A6.18C, MB2716C / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) References: UniProt: P0A552, UniProt: P9WNS5*PLUS, dUTP diphosphatase |
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-Non-polymers , 5 types, 215 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-TRS / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.47 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 3350, magnesium nitrate, TRIS, 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: 1.1271 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 13, 2003 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1271 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→90 Å / Num. all: 39997 / Num. obs: 39997 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 32.6 Å2 / Rsym value: 0.069 / Net I/σ(I): 20 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 5.7 / Num. unique all: 3975 / Rsym value: 0.325 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1SIX Resolution: 1.8→60.86 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.168 / SU ML: 0.068 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.109 / 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: 24.076 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→60.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20 /
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Refinement TLS params. | Method: refined / Origin x: 13.275 Å / Origin y: -8.773 Å / Origin z: -8.998 Å
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