+Open data
-Basic information
Entry | Database: PDB / ID: 3sau | ||||||
---|---|---|---|---|---|---|---|
Title | MUTM Interrogation complex 6 | ||||||
Components |
| ||||||
Keywords | HYDROLASE/DNA / DNA GLYCOSYLASE / DNA REPAIR / DAMAGE SEARCH / TRANSLOCATION / DISULFIDE CROSSLINKING / DNA DAMAGE / DNA-BINDING / GLYCOSIDASE / HYDROLASE / LYASE / METAL-BINDING / MULTIFUNCTIONAL ENZYME / ZINC-FINGER / HYDROLASE-DNA complex | ||||||
Function / homology | Function and homology information DNA-formamidopyrimidine glycosylase / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / base-excision repair / damaged DNA binding / zinc ion binding Similarity search - Function | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Spong, M.C. / Qi, Y. / Verdine, G.L. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Strandwise translocation of a DNA glycosylase on undamaged DNA. Authors: Qi, Y. / Nam, K. / Spong, M.C. / Banerjee, A. / Sung, R.J. / Zhang, M. / Karplus, M. / Verdine, G.L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3sau.cif.gz | 145 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3sau.ent.gz | 109.1 KB | Display | PDB format |
PDBx/mmJSON format | 3sau.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3sau_validation.pdf.gz | 445.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3sau_full_validation.pdf.gz | 447.4 KB | Display | |
Data in XML | 3sau_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | 3sau_validation.cif.gz | 21.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sa/3sau ftp://data.pdbj.org/pub/pdb/validation_reports/sa/3sau | HTTPS FTP |
-Related structure data
Related structure data | 3sarC 3sasC 3satC 3savC 3sawC 3sbjC 3gpxS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 30583.330 Da / Num. of mol.: 1 / Mutation: Q166C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Gene: MUTM / Plasmid: pET24B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) PLYSS References: UniProt: P84131, DNA-(apurinic or apyrimidinic site) lyase |
---|---|
#2: DNA chain | Mass: 4957.231 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHETIC DNA |
#3: DNA chain | Mass: 4900.261 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHETIC DNA |
#4: Chemical | ChemComp-ZN / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.32 % |
---|---|
Crystal grow | Temperature: 291 K / pH: 7 Details: PEG 8K, SODIUM CACODYLATE, GLYCEROL, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 12, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. obs: 52738 / % possible obs: 96.6 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.493 / % possible all: 92.2 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3GPX Resolution: 1.65→25.25 Å / SU ML: 1.1 / σ(F): 0.04 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.19 Å2 / ksol: 0.43 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.6 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→25.25 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|