[English] 日本語
Yorodumi- PDB-2f5s: Catalytically inactive (E3Q) MutM crosslinked to oxoG:C containin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2f5s | ||||||
---|---|---|---|---|---|---|---|
Title | Catalytically inactive (E3Q) MutM crosslinked to oxoG:C containing DNA CC1 | ||||||
Components |
| ||||||
Keywords | hydrolase/DNA / disulfide crosslink / DNA glycosylase / DNA repair / damage search / control complex / hydrolase-DNA COMPLEX | ||||||
Function / homology | Function and homology information DNA-formamidopyrimidine glycosylase / oxidized purine nucleobase lesion 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: 2.35 Å | ||||||
Authors | Banerjee, A. / Santos, W.L. / Verdine, G.L. | ||||||
Citation | Journal: Science / Year: 2006 Title: Structure of a DNA glycosylase searching for lesions. Authors: Banerjee, A. / Santos, W.L. / Verdine, G.L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2f5s.cif.gz | 82.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2f5s.ent.gz | 58 KB | Display | PDB format |
PDBx/mmJSON format | 2f5s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f5/2f5s ftp://data.pdbj.org/pub/pdb/validation_reports/f5/2f5s | HTTPS FTP |
---|
-Related structure data
Related structure data | 2f5nC 2f5oC 2f5pC 2f5qC 1r2yS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: DNA chain | Mass: 4948.217 Da / Num. of mol.: 1 / Source method: obtained synthetically |
---|---|
#2: DNA chain | Mass: 4866.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic DNA containing a backbone modification |
#3: Protein | Mass: 30713.537 Da / Num. of mol.: 1 / Mutation: E3Q, Q166C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Plasmid: Pet24b / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 pLysS References: UniProt: P84131, DNA-formamidopyrimidine glycosylase |
#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: 2.68 Å3/Da / Density % sol: 54.17 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 350K, temperature 277K |
-Data collection
Diffraction | Mean temperature: 77 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.976 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 6, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. obs: 17996 / % possible obs: 95 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 27.1 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.35→2.43 Å / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.7 / Num. unique all: 1783 / % possible all: 97.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1R2Y Resolution: 2.35→37.99 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 259602.7 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.2366 Å2 / ksol: 0.339025 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.2 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→37.99 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.35→2.5 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|