+Open data
-Basic information
Entry | Database: PDB / ID: 3zoq | ||||||
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Title | Structure of BsUDG-p56 complex | ||||||
Components |
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Keywords | HYDROLASE/VIRAL PROTEIN / HYDROLASE-VIRAL PROTEIN COMPLEX | ||||||
Function / homology | Function and homology information base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / biological process involved in interaction with host / uracil DNA N-glycosylase activity / cytoplasm Similarity search - Function | ||||||
Biological species | BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168 (bacteria) BACILLUS PHAGE PHI29 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Banos-Sanz, J.I. / Mojardin, L. / Sanz-Aparicio, J. / Gonzalez, B. / Salas, M. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2013 Title: Crystal Structure and Functional Insights Into Uracil-DNA Glycosylase Inhibition by Phage Phi29 DNA Mimic Protein P56 Authors: Banos-Sanz, J.I. / Mojardin, L. / Sanz-Aparicio, J. / Lazaro, J.M. / Villar, L. / Serrano-Heras, G. / Gonzalez, B. / Salas, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zoq.cif.gz | 174.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zoq.ent.gz | 138.7 KB | Display | PDB format |
PDBx/mmJSON format | 3zoq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zo/3zoq ftp://data.pdbj.org/pub/pdb/validation_reports/zo/3zoq | HTTPS FTP |
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-Related structure data
Related structure data | 3zorC 2eugS 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
#1: Protein | Mass: 26083.721 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168 (bacteria) Plasmid: PT7-4-UDG-WT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P39615, uracil-DNA glycosylase | ||||||
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#2: Protein | Mass: 6571.311 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS PHAGE PHI29 (virus) / Plasmid: PT7-3-P56-F29 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q38503 #3: Chemical | ChemComp-GOL / | #4: Chemical | ChemComp-CL / | #5: 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: 2.34 Å3/Da / Density % sol: 47.52 % / Description: NONE |
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Crystal grow | Temperature: 277 K / pH: 8.5 Details: 19% PEG 8000, 0.1 M TRIS-HCL, PH 8.5, 0.25 M MAGNESIUM CHLORIDE AT 277 K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 14, 2011 / Details: PT COATED SI MIRRORS |
Radiation | Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→23.86 Å / Num. obs: 65433 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 1.45→1.53 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 4.6 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2EUG Resolution: 1.45→55.62 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.026 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.063 / 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: 19.093 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→55.62 Å
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Refine LS restraints |
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