+Open data
-Basic information
Entry | Database: PDB / ID: 1bnk | ||||||
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Title | HUMAN 3-METHYLADENINE DNA GLYCOSYLASE COMPLEXED TO DNA | ||||||
Components |
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Keywords | HYDROLASE/DNA / DNA REPAIR / DNA GLYCOSYLASE / HYDROLASE-DNA COMPLEX | ||||||
Function / homology | Function and homology information alkylbase DNA N-glycosylase activity / DNA-7-methyladenine glycosylase activity / DNA-3-methylguanine glycosylase activity / DNA-3-methyladenine glycosylase II / DNA-7-methylguanine glycosylase activity / DNA-3-methyladenine glycosylase activity / depurination / DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 / DNA alkylation repair ...alkylbase DNA N-glycosylase activity / DNA-7-methyladenine glycosylase activity / DNA-3-methylguanine glycosylase activity / DNA-3-methyladenine glycosylase II / DNA-7-methylguanine glycosylase activity / DNA-3-methyladenine glycosylase activity / depurination / DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 / DNA alkylation repair / mitochondrial nucleoid / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / base-excision repair / damaged DNA binding / nucleoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å | ||||||
Authors | Lau, A.Y. / Schaerer, O.D. / Samson, L. / Verdine, G.L. / Ellenberger, T. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 1998 Title: Crystal structure of a human alkylbase-DNA repair enzyme complexed to DNA: mechanisms for nucleotide flipping and base excision. Authors: Lau, A.Y. / Scharer, O.D. / Samson, L. / Verdine, G.L. / Ellenberger, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bnk.cif.gz | 67.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bnk.ent.gz | 46.9 KB | Display | PDB format |
PDBx/mmJSON format | 1bnk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bnk_validation.pdf.gz | 378.6 KB | Display | wwPDB validaton report |
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Full document | 1bnk_full_validation.pdf.gz | 386.9 KB | Display | |
Data in XML | 1bnk_validation.xml.gz | 6.9 KB | Display | |
Data in CIF | 1bnk_validation.cif.gz | 9.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bn/1bnk ftp://data.pdbj.org/pub/pdb/validation_reports/bn/1bnk | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 3832.501 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 3975.611 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Protein | Mass: 24051.623 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Organ: LIVER / Plasmid: PLM1-AAG / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Gene (production host): AAG / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: P29372, DNA-3-methyladenine glycosylase II |
#4: 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: 2.49 Å3/Da / Density % sol: 56 % Description: DATA WERE COLLECTED USING THE OSCILLATION METHOD | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 113 K | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.5418, 1.0100, 0.9787, 0.9784, 0.9500 | ||||||||||||||||||
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 1998 / Details: MIRRORS | ||||||||||||||||||
Radiation | Monochromator: NI FILTER / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.7→30 Å / Num. obs: 9321 / % possible obs: 100 % / Redundancy: 9 % / Rsym value: 0.046 / Net I/σ(I): 15 | ||||||||||||||||||
Reflection shell | Resolution: 2.7→2.82 Å / Redundancy: 9 % / Mean I/σ(I) obs: 10 / Rsym value: 0.145 / % possible all: 100 | ||||||||||||||||||
Reflection | *PLUS % possible obs: 99.6 % / Num. measured all: 269241 / Rmerge(I) obs: 0.046 | ||||||||||||||||||
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.176 / Mean I/σ(I) obs: 12.2 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.7→8 Å / Data cutoff high rms absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 3
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Refinement step | Cycle: LAST / Resolution: 2.7→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.79 Å / Total num. of bins used: 10 /
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.3C / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 8 Å / σ(F): 3 / % reflection Rfree: 10 % / Rfactor Rfree: 0.26 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.302 / Rfactor Rwork: 0.265 |