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Yorodumi- PDB-4ai4: crystal structure of E38Q mutant of 3-methyladenine DNA glycosyla... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ai4 | ||||||
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Title | crystal structure of E38Q mutant of 3-methyladenine DNA glycosylase I from Staphylococcus aureus | ||||||
Components | DNA-3-METHYLADENINE GLYCOSYLASE I | ||||||
Keywords | HYDROLASE / DNA REPAIR | ||||||
Function / homology | Hypothetical protein; domain 2 / Endonuclease III; domain 1 / Orthogonal Bundle / Mainly Alpha / : Function and homology information | ||||||
Biological species | STAPHYLOCOCCUS AUREUS SUBSP. AUREUS MSSA476 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.73 Å | ||||||
Authors | Zhu, X. / Naismith, J.H. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2012 Title: A Model for 3-Methyladenine Recognition by 3-Methyladenine DNA Glycosylase I (Tag) from Staphylococcus Aureus. Authors: Zhu, X. / Yan, X. / Carter, L.G. / Liu, H. / Graham, S. / Coote, P.J. / Naismith, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ai4.cif.gz | 91.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ai4.ent.gz | 69.3 KB | Display | PDB format |
PDBx/mmJSON format | 4ai4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ai4_validation.pdf.gz | 419 KB | Display | wwPDB validaton report |
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Full document | 4ai4_full_validation.pdf.gz | 418.9 KB | Display | |
Data in XML | 4ai4_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | 4ai4_validation.cif.gz | 14.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ai/4ai4 ftp://data.pdbj.org/pub/pdb/validation_reports/ai/4ai4 | HTTPS FTP |
-Related structure data
Related structure data | 4ai5C 4aiaC 2jg6S 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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 21572.498 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) STAPHYLOCOCCUS AUREUS SUBSP. AUREUS MSSA476 (bacteria) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43 References: UniProt: Q6G8R1, DNA-3-methyladenine glycosylase I | ||||
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#2: Chemical | ChemComp-ZN / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 58 % / Description: NONE |
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Crystal grow | pH: 8.5 / Details: pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Dec 20, 2011 / Details: OSMIC |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→36.09 Å / Num. obs: 20849 / % possible obs: 82.5 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 20 |
Reflection shell | Resolution: 1.73→1.77 Å / Redundancy: 2 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.5 / % possible all: 26.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2JG6 Resolution: 1.73→53.67 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.854 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.932 Å2
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Refinement step | Cycle: LAST / Resolution: 1.73→53.67 Å
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Refine LS restraints |
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