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Yorodumi- PDB-7lxj: Bacillus cereus DNA glycosylase AlkD bound to a duocarmycin SA-ad... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7lxj | ||||||
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Title | Bacillus cereus DNA glycosylase AlkD bound to a duocarmycin SA-adenine nucleobase adduct and DNA containing an abasic site | ||||||
Components |
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Keywords | HYDROLASE/DNA/ANTIBIOTIC / DNA Repair / Base Excision Repair / Antibiotic Self-Resistance / Bulky DNA Adduct / Secondary Metabolite / DNA BINDING PROTEIN / HYDROLASE-DNA-ANTIBIOTIC complex | ||||||
Function / homology | DNA alkylation repair enzyme / DNA alkylation repair enzyme / Armadillo-type fold / Chem-YNY / DNA / DNA-7-methylguanine glycosylase Function and homology information | ||||||
Biological species | Bacillus cereus (bacteria) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å | ||||||
Authors | Mullins, E.A. / Eichman, B.F. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2021 Title: Structural evolution of a DNA repair self-resistance mechanism targeting genotoxic secondary metabolites. Authors: Mullins, E.A. / Dorival, J. / Tang, G.L. / Boger, D.L. / 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 | 7lxj.cif.gz | 187 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lxj.ent.gz | 144.7 KB | Display | PDB format |
PDBx/mmJSON format | 7lxj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7lxj_validation.pdf.gz | 778.4 KB | Display | wwPDB validaton report |
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Full document | 7lxj_full_validation.pdf.gz | 780.1 KB | Display | |
Data in XML | 7lxj_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 7lxj_validation.cif.gz | 19.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lx/7lxj ftp://data.pdbj.org/pub/pdb/validation_reports/lx/7lxj | HTTPS FTP |
-Related structure data
Related structure data | 7lxhC 3bvsS 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: 28578.043 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: bcere0015_46090 / Plasmid: PBG103 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): HMS174(DE3) / References: UniProt: C2T7T7 |
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-DNA chain , 2 types, 2 molecules BC
#2: DNA chain | Mass: 2656.739 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#3: DNA chain | Mass: 2697.771 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 192 molecules
#4: Chemical | #5: Chemical | ChemComp-YNY / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.87 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 24% (w/v) PEG 8000, 50 mM HEPES pH 7.0, and 50 mM calcium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Oct 8, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.93→50 Å / Num. obs: 22584 / % possible obs: 99.9 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.028 / Rrim(I) all: 0.073 / Χ2: 1.061 / Net I/av σ(I): 24.7 / Net I/σ(I): 10.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3BVS Resolution: 1.93→44.434 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.44 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 243.88 Å2 / Biso mean: 45.5047 Å2 / Biso min: 17.29 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.93→44.434 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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