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Yorodumi- PDB-1f4r: CRYSTAL STRUCTURE OF THE HUMAN AAG DNA REPAIR GLYCOSYLASE COMPLEX... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1f4r | ||||||
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Title | CRYSTAL STRUCTURE OF THE HUMAN AAG DNA REPAIR GLYCOSYLASE COMPLEXED WITH 1,N6-ETHENOADENINE-DNA | ||||||
Components |
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Keywords | HYDROLASE/DNA / PROTEIN-DNA COMPLEX / 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 / Resolution: 2.4 Å | ||||||
Authors | Lau, A.Y. / Wyatt, M.D. / Glassner, B.J. / Samson, L.D. / Ellenberger, T. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2000 Title: Molecular basis for discriminating between normal and damaged bases by the human alkyladenine glycosylase, AAG. Authors: Lau, A.Y. / Wyatt, M.D. / Glassner, B.J. / Samson, L.D. / Ellenberger, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1f4r.cif.gz | 68 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f4r.ent.gz | 46.9 KB | Display | PDB format |
PDBx/mmJSON format | 1f4r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1f4r_validation.pdf.gz | 384.1 KB | Display | wwPDB validaton report |
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Full document | 1f4r_full_validation.pdf.gz | 389.9 KB | Display | |
Data in XML | 1f4r_validation.xml.gz | 6.6 KB | Display | |
Data in CIF | 1f4r_validation.cif.gz | 9.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f4/1f4r ftp://data.pdbj.org/pub/pdb/validation_reports/f4/1f4r | HTTPS FTP |
-Related 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: 3990.618 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 1,N6-ETHENOADENINE-DNA |
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#2: DNA chain | Mass: 3975.611 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Protein | Mass: 24328.916 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PLM1 / Production host: Escherichia coli (E. coli) References: UniProt: P29372, DNA-3-methyladenine glycosylase I |
#4: Chemical | ChemComp-NA / |
#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: 2.32 Å3/Da / Density % sol: 47.03 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 4000, magnesium chloride, Tris-HCl, glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 22 ℃ | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.01 |
Detector | Type: PHILLIPS / Detector: CCD / Date: Jan 1, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.01 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→500 Å / Num. all: 12607 / Num. obs: 12526 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 8 % / Biso Wilson estimate: 45.6 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 55.4 |
Reflection shell | Resolution: 2.4→2.51 Å / Redundancy: 7 % / Rmerge(I) obs: 0.137 / Num. unique all: 1478 / % possible all: 99.7 |
Reflection | *PLUS Num. obs: 12133 / Num. measured all: 167384 |
Reflection shell | *PLUS % possible obs: 99.7 % / Mean I/σ(I) obs: 12.1 |
-Processing
Software |
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Refinement | Resolution: 2.4→500 Å / Cross valid method: THROUGHOUT / σ(F): 4 / σ(I): 2 / Stereochemistry target values: Engh & Huber Details: Used Powell conjugate gradient minimization and torsion angle-restrained molecular dynamics
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Refinement step | Cycle: LAST / Resolution: 2.4→500 Å
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Refine LS restraints |
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