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- PDB-4ai5: Crystal structure of Y16F of 3-methyladenine DNA glycosylase I (T... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ai5 | ||||||
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Title | Crystal structure of Y16F of 3-methyladenine DNA glycosylase I (TAG) in complex with 3-methyladenine | ||||||
![]() | DNA-3-METHYLADENINE GLYCOSYLASE I | ||||||
![]() | HYDROLASE / 3-METHYLADENINE RECOGNITION / DNA REPAIR / 3-METHYLADENINE TAUTOMER | ||||||
Function / homology | Hypothetical protein; domain 2 / Endonuclease III; domain 1 / Orthogonal Bundle / Mainly Alpha / 3-METHYL-3H-PURIN-6-YLAMINE / : ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Zhu, X. / Naismith, J.H. | ||||||
![]() | ![]() 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.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 389.3 KB | Display | ![]() |
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PDB format | ![]() | 321.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4ai4C ![]() 4aiaC ![]() 2jg6S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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5 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 21557.482 Da / Num. of mol.: 5 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: Q6G8R1, DNA-3-methyladenine glycosylase I #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-ADK / #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, TYR 16 TO PHE ENGINEERED RESIDUE IN CHAIN B, TYR 16 TO PHE ...ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.25 % / 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: ![]() |
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: 2.22→50 Å / Num. obs: 47714 / % possible obs: 95.5 % / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 28 |
Reflection shell | Resolution: 2.22→2.26 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 11 / % possible all: 89.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2JG6 Resolution: 2.22→179.29 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.915 / SU B: 9.03 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.339 / ESU R Free: 0.211 / 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: 18.736 Å2
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Refinement step | Cycle: LAST / Resolution: 2.22→179.29 Å
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Refine LS restraints |
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