+Open data
-Basic information
Entry | Database: PDB / ID: 3ogd | ||||||
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Title | AlkA Undamaged DNA Complex: Interrogation of a G*:C base pair | ||||||
Components |
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Keywords | HYDROLASE/DNA / helix-hairpin-helix / DNA repair / Alkylation / HYDROLASE-DNA complex | ||||||
Function / homology | Function and homology information alkylated DNA binding / 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 / base-excision repair, AP site formation / DNA alkylation repair / protein-DNA complex ...alkylated DNA binding / 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 / base-excision repair, AP site formation / DNA alkylation repair / protein-DNA complex / base-excision repair / DNA repair / DNA damage response / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Bowman, B.R. / Lee, S. / Wang, S. / Verdine, G.L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Structure of Escherichia coli AlkA in Complex with Undamaged DNA. Authors: Bowman, B.R. / Lee, S. / Wang, S. / 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 | 3ogd.cif.gz | 82.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ogd.ent.gz | 58.2 KB | Display | PDB format |
PDBx/mmJSON format | 3ogd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ogd_validation.pdf.gz | 444 KB | Display | wwPDB validaton report |
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Full document | 3ogd_full_validation.pdf.gz | 451.6 KB | Display | |
Data in XML | 3ogd_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 3ogd_validation.cif.gz | 17.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/og/3ogd ftp://data.pdbj.org/pub/pdb/validation_reports/og/3ogd | HTTPS FTP |
-Related structure data
Related structure data | 3oh6C 3oh9C 1dizS 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
#1: Protein | Mass: 32134.967 Da / Num. of mol.: 1 / Mutation: L125C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: aidA, alkA, b2068, JW2053 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RD2 References: UniProt: P04395, DNA-3-methyladenine glycosylase II |
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#2: DNA chain | Mass: 2755.823 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: DNA chain | Mass: 2845.539 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.07 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 25-29% peg3350, 100mM Bis-Tris 6.0-6.6, 200mM LiSo, 3% 6-aminocaproic acid, pH 6.0-6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K PH range: 6.0-6.5 |
-Data collection
Diffraction | Mean temperature: 77 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9197 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 25, 2008 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9197 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.779→50 Å / Num. obs: 12042 / % possible obs: 99.5 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.072 / Χ2: 1.349 / Net I/σ(I): 12.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DIZ Resolution: 2.8→44.177 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7759 / SU ML: 2.58 / σ(F): 0.16 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.543 Å2 / ksol: 0.286 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 207 Å2 / Biso mean: 102.6048 Å2 / Biso min: 60.54 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→44.177 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: 7
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