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Yorodumi- PDB-3jr5: MutM lesion recognition control complex with N174C crosslinking site -
+Open data
-Basic information
Entry | Database: PDB / ID: 3jr5 | ||||||
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Title | MutM lesion recognition control complex with N174C crosslinking site | ||||||
Components |
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Keywords | Lyase/DNA / DNA glycosylase / DNA repair / damage search / base extrusion / disulfide crosslinking / DNA damage / DNA-binding / Glycosidase / Hydrolase / Lyase / Metal-binding / Multifunctional enzyme / Zinc-finger / Lyase-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: 1.704 Å | ||||||
Authors | Qi, Y. / Spong, M.C. / Verdine, G.L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Entrapment and structure of an extrahelical guanine attempting to enter the active site of a bacterial DNA glycosylase, MutM. Authors: Qi, Y. / Spong, M.C. / Nam, K. / Karplus, M. / 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 | 3jr5.cif.gz | 94.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3jr5.ent.gz | 66.9 KB | Display | PDB format |
PDBx/mmJSON format | 3jr5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3jr5_validation.pdf.gz | 437.7 KB | Display | wwPDB validaton report |
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Full document | 3jr5_full_validation.pdf.gz | 438 KB | Display | |
Data in XML | 3jr5_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | 3jr5_validation.cif.gz | 23.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jr/3jr5 ftp://data.pdbj.org/pub/pdb/validation_reports/jr/3jr5 | HTTPS FTP |
-Related structure data
Related structure data | 3jr4C 1r2yS C: citing same article (ref.) S: Starting model for refinement |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 30596.373 Da / Num. of mol.: 1 / Fragment: MutM / Mutation: N174C 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): BL21(DE3) PlysS References: UniProt: P84131, DNA-(apurinic or apyrimidinic site) lyase |
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-DNA chain , 2 types, 2 molecules BC
#2: DNA chain | Mass: 4948.217 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#3: DNA chain | Mass: 4925.274 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Non-polymers , 3 types, 297 molecules
#4: Chemical | ChemComp-ZN / |
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#5: Chemical | ChemComp-GOL / |
#6: 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: 2.74 Å3/Da / Density % sol: 55.07 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 8K, sodium cacodylate, glycerol, pH 7.0, vapor diffusion, hanging drop, temperature 298K | ||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.29 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC / Detector: CCD / Date: Feb 10, 2008 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.29 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→50 Å / Num. obs: 48192 / % possible obs: 98.4 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.074 / Χ2: 1.031 / Net I/σ(I): 12.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1R2Y Resolution: 1.704→38.027 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.2 / σ(F): 1 / Stereochemistry target values: ML
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Solvent computation | Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.963 Å2 / ksol: 0.368 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 130.31 Å2 / Biso mean: 25.972 Å2 / Biso min: 8.67 Å2
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Refinement step | Cycle: LAST / Resolution: 1.704→38.027 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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