[English] 日本語
Yorodumi- PDB-1lqm: ESCHERICHIA COLI URACIL-DNA GLYCOSYLASE COMPLEX WITH URACIL-DNA G... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lqm | ||||||
---|---|---|---|---|---|---|---|
Title | ESCHERICHIA COLI URACIL-DNA GLYCOSYLASE COMPLEX WITH URACIL-DNA GLYCOSYLASE INHIBITOR PROTEIN | ||||||
Components |
| ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / GLYCOSYLASE / INHIBITOR / DNA REPAIR / BASE EXCISION / COMPLEX (HYDROLASE-INHIBITOR) / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / uracil DNA N-glycosylase activity / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) Bacillus phage PBS2 (virus) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Saikrishnan, K. / Sagar, M.B. / Ravishankar, R. / Roy, S. / Purnapatre, K. / Varshney, U. / Vijayan, M. | ||||||
Citation | 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. #1: 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. / Sagar, M.B. / Roy, S. / Purnapatre, K. / Handa, P. / Varshney, U. / Vijayan, M. #2: Journal: Protein Expr.Purif. / Year: 1998 Title: Use of a coupled transcriptional system for consistent overexpression and purification of UDG-UGI complex and ugi from Escherichia coli Authors: Roy, S. / Purnapatre, K. / Handa, P. / Boyanapalli, M. / Varshney, U. #3: Journal: J.Mol.Biol. / Year: 1999 Title: Protein mimicry of DNA from crystal structures of the uracil-DNA glycosylase inhibitor protein and its complex with Escherichia coli uracil-DNA glycosylase. Authors: Putnam, C.D. / Shroyer, M.J.N. / Lundquist, A.J. / Mol, C.D. / Arvai, A.S. / Mosbaugh, D.W. / Tainer, J.A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1lqm.cif.gz | 223.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1lqm.ent.gz | 185 KB | Display | PDB format |
PDBx/mmJSON format | 1lqm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lq/1lqm ftp://data.pdbj.org/pub/pdb/validation_reports/lq/1lqm | HTTPS FTP |
---|
-Related structure data
Related structure data | 1lqgC 1lqjC 1uugS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
2 |
| ||||||||||
3 |
| ||||||||||
4 |
| ||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 25725.182 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) References: UniProt: P12295, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds #2: Protein | Mass: 9482.674 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus phage PBS2 (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: P14739 #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.56 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: 20mM imidazole-maleate, 10% PEG 4000, pH 7.6, VAPOR DIFFUSION, HANGING DROP at 293K, temperature 293.0K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 281 K | ||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→15 Å / Num. all: 21106 / Num. obs: 21106 / % possible obs: 87.6 % / Observed criterion σ(I): 0 / Rsym value: 0.167 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 3.2→3.31 Å / Mean I/σ(I) obs: 1.4 / Rsym value: 0.398 / % possible all: 79.3 |
Reflection | *PLUS Highest resolution: 3.2 Å / Num. measured all: 94765 / Rmerge(I) obs: 0.167 |
Reflection shell | *PLUS % possible obs: 79.3 % / Rmerge(I) obs: 0.398 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1UUG Resolution: 3.2→15 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.5 Å2 | |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→15 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 3.2→3.4 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
| |||||||||||||||||||||||||
Xplor file |
| |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 15 Å / Rfactor Rfree: 0.26 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
|