+Open data
-Basic information
Entry | Database: PDB / ID: 2jhj | ||||||
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Title | 3-methyladenine dna-glycosylase from Archaeoglobus fulgidus | ||||||
Components | 3-METHYLADENINE DNA-GLYCOSYLASE | ||||||
Keywords | HYDROLASE / ALKA / DNA REPAIR / N1-METHYLADENINE / N3-METHYLCYTOSINE / HYPERTHERMOPHILES / ARCHAEOGLOBUS FULGIDUS | ||||||
Function / homology | Function and homology information | ||||||
Biological species | ARCHAEOGLOBUS FULGIDUS (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Leiros, I. / Nabong, M.P. / Grosvik, K. / Ringvoll, J. / Haugland, G.T. / Uldal, L. / Reite, K. / Olsbu, I.K. / Knaevelsrud, I. / Moe, E. ...Leiros, I. / Nabong, M.P. / Grosvik, K. / Ringvoll, J. / Haugland, G.T. / Uldal, L. / Reite, K. / Olsbu, I.K. / Knaevelsrud, I. / Moe, E. / Andersen, O.A. / Birkeland, N.K. / Ruoff, P. / Klungland, A. / Bjelland, S. | ||||||
Citation | Journal: Embo J. / Year: 2007 Title: Structural Basis for Enzymatic Excision of N1-Methyladenine and N3-Methylcytosine from DNA Authors: Leiros, I. / Nabong, M.P. / Grosvik, K. / Ringvoll, J. / Haugland, G.T. / Uldal, L. / Reite, K. / Olsbu, I.K. / Knaevelsrud, I. / Moe, E. / Andersen, O.A. / Birkeland, N.K. / Ruoff, P. / ...Authors: Leiros, I. / Nabong, M.P. / Grosvik, K. / Ringvoll, J. / Haugland, G.T. / Uldal, L. / Reite, K. / Olsbu, I.K. / Knaevelsrud, I. / Moe, E. / Andersen, O.A. / Birkeland, N.K. / Ruoff, P. / Klungland, A. / Bjelland, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jhj.cif.gz | 142.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jhj.ent.gz | 112.6 KB | Display | PDB format |
PDBx/mmJSON format | 2jhj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jh/2jhj ftp://data.pdbj.org/pub/pdb/validation_reports/jh/2jhj | HTTPS FTP |
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-Related structure data
Related structure data | 2jhnSC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 34299.555 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea) / Strain: VC 16 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: O28163, DNA-3-methyladenine glycosylase II #2: Chemical | ChemComp-NA / #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
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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: 2.7 Å3/Da / Density % sol: 54 % Description: THE STARTING MODEL WAS A MERCURY DERIVATIVE SOLVED BY SAD |
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Crystal grow | Details: 0.1M BICINE, PH9.0 10% W/V PEG20000 2% V/V DIOXANE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.919 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 13, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.919 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 53742 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 19.75 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2JHN Resolution: 1.9→12 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.924 / SU B: 3.333 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. A290-A294 AND B290-B293 ARE DISORDERED THE TWO PROTEIN MONOMERS IN THE ASYMMETRIC UNIT ARE RELATED BY A PSEUDO-TRANSLATIONAL VECTOR (0.5, 0. ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. A290-A294 AND B290-B293 ARE DISORDERED THE TWO PROTEIN MONOMERS IN THE ASYMMETRIC UNIT ARE RELATED BY A PSEUDO-TRANSLATIONAL VECTOR (0.5, 0.45, 0.5). THE TWO MONOMERS WERE REFINED INDIVIDUALLY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.57 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→12 Å
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Refine LS restraints |
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