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Yorodumi- PDB-2jg6: CRYSTAL STRUCTURE OF A 3-METHYLADENINE DNA GLYCOSYLASE I FROM STA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jg6 | ||||||
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Title | CRYSTAL STRUCTURE OF A 3-METHYLADENINE DNA GLYCOSYLASE I FROM STAPHYLOCOCCUS AUREUS | ||||||
Components | DNA-3-METHYLADENINE GLYCOSIDASE | ||||||
Keywords | HYDROLASE / GLYCOSIDASE / 3-METHYLADENINE-DNA-GLYCOSYLASE-I | ||||||
Function / homology | Function and homology information DNA-3-methyladenine glycosylase I / DNA-3-methyladenine glycosylase activity / base-excision repair / metal ion binding Similarity search - Function | ||||||
Biological species | STAPHYLOCOCCUS AUREUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å | ||||||
Authors | Yan, X. / Carter, L.G. / Liu, H. / Dorward, M. / McMahon, S.A. / Johnson, K.A. / Oke, M. / Coote, P.J. / Naismith, J.H. | ||||||
Citation | Journal: J.Struct.Funct.Genomics / Year: 2010 Title: The Scottish Structural Proteomics Facility: Targets, Methods and Outputs. Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / ...Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / Falconer, H. / Powers, H. / Overton, I.M. / Van Niekerk, C.A.J. / Peng, X. / Patel, P. / Garrett, R.A. / Prangishvili, D. / Botting, C.H. / Coote, P.J. / Dryden, D.T.F. / Barton, G.J. / Schwarz-Linek, U. / Challis, G.L. / Taylor, G.L. / White, M.F. / Naismith, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jg6.cif.gz | 95.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jg6.ent.gz | 73.6 KB | Display | PDB format |
PDBx/mmJSON format | 2jg6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2jg6_validation.pdf.gz | 399.8 KB | Display | wwPDB validaton report |
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Full document | 2jg6_full_validation.pdf.gz | 399.8 KB | Display | |
Data in XML | 2jg6_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | 2jg6_validation.cif.gz | 16.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jg/2jg6 ftp://data.pdbj.org/pub/pdb/validation_reports/jg/2jg6 | HTTPS FTP |
-Related structure data
Related structure data | 2ivyC 2jg5C 2vw8C 2vxzC 2wj9C 2x0oC 2x3dC 2x3eC 2x3fC 2x3gC 2x3lC 2x3mC 2x3nC 2x3oC 2x48C 2x4gC 2x4hC 2x4iC 2x4jC 2x4kC 2x4lC 2x5cC 2x5dC 2x5fC 2x5gC 2x5hC 2x5pC 2x5qC 2x5rC 2x5tC 2x7bC 2x7iC 2xu2C 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: 21445.354 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Strain: MSSA476 / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C43 References: UniProt: Q9RL93, DNA-3-methyladenine glycosylase I |
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#2: Chemical | ChemComp-ZN / |
#3: 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: 3.04 Å3/Da / Density % sol: 59.57 % / Description: STRUCTURE SOLVED USING ZINC SIGNAL |
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Crystal grow | pH: 7.5 / Details: 1,6 M TRISODIUM CITRATE, pH 7.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.282 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 8, 2006 / Details: MIRRORS |
Radiation | Monochromator: SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.282 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 26056 / % possible obs: 97.1 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 23 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3.6 / % possible all: 76 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.7→29.81 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.938 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.09 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.74 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→29.81 Å
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Refine LS restraints |
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