+Open data
-Basic information
Entry | Database: PDB / ID: 2f5p | ||||||
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Title | MutM crosslinked to undamaged DNA sampling A:T base pair IC2 | ||||||
Components |
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Keywords | hydrolase/DNA / disulfide crosslink / DNA glycosylase / DNA repair / damage search / 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) Synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2f5p.cif.gz | 82.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2f5p.ent.gz | 58.6 KB | Display | PDB format |
PDBx/mmJSON format | 2f5p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2f5p_validation.pdf.gz | 444.4 KB | Display | wwPDB validaton report |
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Full document | 2f5p_full_validation.pdf.gz | 446.5 KB | Display | |
Data in XML | 2f5p_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 2f5p_validation.cif.gz | 19.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f5/2f5p ftp://data.pdbj.org/pub/pdb/validation_reports/f5/2f5p | HTTPS FTP |
-Related structure data
Related structure data | 2f5nC 2f5oC 2f5qC 2f5sC 1r2yS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 4963.228 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others) |
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#2: DNA chain | Mass: 4834.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others) |
#3: Protein | Mass: 30714.521 Da / Num. of mol.: 1 / Mutation: 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 |
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-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.53 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: VAPOR DIFFUSION, HANGING DROP, pH 7.0, temperature 350K, temperature 277K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 4, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 30052 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 3.6 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1R2Y Resolution: 2→41.72 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 324043.43 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.9767 Å2 / ksol: 0.358353 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→41.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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