[English] 日本語
Yorodumi- PDB-3a7n: Crystal structure of uracil-DNA glycosylase from Mycobacterium tu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3a7n | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of uracil-DNA glycosylase from Mycobacterium tuberculosis | ||||||
Components | Uracil-DNA glycosylase | ||||||
Keywords | HYDROLASE / Ung-Ugi interactions / Ung-DNA complex / citrate as protein ligand / ligand binding / inhibitor design / DNA damage / DNA repair / Glycosidase | ||||||
Function / homology | Function and homology information base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / uracil DNA N-glycosylase activity / base-excision repair / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis H37Rv (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Kaushal, P.S. / Talawar, R.K. / Varshney, U. / Vijayan, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2010 Title: Structure of uracil-DNA glycosylase from Mycobacterium tuberculosis: insights into interactions with ligands Authors: Kaushal, P.S. / Talawar, R.K. / Varshney, U. / Vijayan, M. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2008 Title: Unique features of the structure and interactions of mycobacterial uracil-DNA glycosylase: structure of a complex of the Mycobacterium tuberculosis enzyme in comparison with those from other sources Authors: Kaushal, P.S. / Talawar, R.K. / Krishna, P.D.V. / Varshney, U. / Vijayan, M. #2: Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: Domain closure and action of uracil DNA glycosylase (UDG): structures of new crystal forms containing the Escherichia coli enzyme and a comparative study of the known structures involving UDG Authors: Saikrishnan, K. / Bidya Sagar, M. / Ravishankar, R. / Roy, S. / Purnapatre, K. / Handa, P. / Varshney, U. / Vijayan, M. #3: Journal: Nucleic Acids Res. / Year: 1998 Title: X-ray analysis of a complex of Escherichia coli uracil DNA glycosylase (EcUDG) with a proteinaceous inhibitor. The structure elucidation of a prokaryotic UDG Authors: Ravishankar, R. / Bidya Sagar, M. / Roy, S. / Purnapatre, K. / Handa, P. / Varshney, U. / Vijayan, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3a7n.cif.gz | 64 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3a7n.ent.gz | 45.9 KB | Display | PDB format |
PDBx/mmJSON format | 3a7n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a7/3a7n ftp://data.pdbj.org/pub/pdb/validation_reports/a7/3a7n | HTTPS FTP |
---|
-Related structure data
Related structure data | 2zhxS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 25813.543 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Strain: H37RV / Gene: ung, Rv2976c / Plasmid: PRSETB MTUUDG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P67071, UniProt: P9WFQ9*PLUS, uridine nucleosidase | ||
---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.51 % |
---|---|
Crystal grow | Temperature: 298 K / Method: microbatch / pH: 7 Details: 1.8M tri-ammonium citrate pH 7.0, 10% isopropanol, microbatch, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 10, 2008 / Details: mirrors |
Radiation | Monochromator: OSMIC MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→30 Å / Num. all: 18628 / Num. obs: 18238 / % possible obs: 98.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 30 Å2 / Rsym value: 0.1 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 2583 / Rsym value: 0.493 / % possible all: 97.7 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ZHX Resolution: 1.95→26.24 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.946 / SU B: 6.309 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.059 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→26.24 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.95→2 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|