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Yorodumi- PDB-3jxy: Bacillus cereus Alkylpurine DNA Glycosylase AlkD Bound to DNA Con... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3jxy | ||||||
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Title | Bacillus cereus Alkylpurine DNA Glycosylase AlkD Bound to DNA Containing a GT Mismatch | ||||||
Components |
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Keywords | hydrolase/DNA / HEAT repeat / DNA binding / DNA glycosylase / DNA alkylation / lyase-DNA COMPLEX / hydrolase-DNA COMPLEX | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus cereus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Rubinson, E.H. / Eichman, B.F. | ||||||
Citation | Journal: Nature / Year: 2010 Title: An unprecedented nucleic acid capture mechanism for excision of DNA damage. Authors: Rubinson, E.H. / Gowda, A.S. / Spratt, T.E. / Gold, B. / Eichman, B.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3jxy.cif.gz | 161.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3jxy.ent.gz | 122.7 KB | Display | PDB format |
PDBx/mmJSON format | 3jxy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3jxy_validation.pdf.gz | 423.3 KB | Display | wwPDB validaton report |
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Full document | 3jxy_full_validation.pdf.gz | 425.4 KB | Display | |
Data in XML | 3jxy_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 3jxy_validation.cif.gz | 27.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jx/3jxy ftp://data.pdbj.org/pub/pdb/validation_reports/jx/3jxy | HTTPS FTP |
-Related structure data
Related structure data | 3jx7SC 3jxzC 3jy1C 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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Details | biological unit is asymmetric unit |
-Components
#1: Protein | Mass: 27724.082 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 10987 / Gene: AlkD, BC_4913 / Plasmid: pBG103 / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 / References: UniProt: Q816E8 |
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#2: DNA chain | Mass: 3728.429 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: DNA chain | Mass: 3614.354 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#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: 2.26 Å3/Da / Density % sol: 45.69 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M BisTris pH 5.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9785 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 11, 2007 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→35.3 Å / Num. all: 49763 / Num. obs: 46379 / % possible obs: 93.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 17.2 Å2 / Rsym value: 0.043 / Net I/σ(I): 22 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 4.9 / Rsym value: 0.186 / % possible all: 87.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB 3JX7 Resolution: 1.5→28.164 Å / SU ML: 0.17 / σ(F): 1.42 / Phase error: 16.75 / 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: 66.521 Å2 / ksol: 0.404 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→28.164 Å
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Refine LS restraints |
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LS refinement shell |
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