+Open data
-Basic information
Entry | Database: PDB / ID: 5ays | |||||||||
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Title | Crystal structure of SAUGI/HSV UDG complex | |||||||||
Components |
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Keywords | HYDROLASE INHIBITOR / DNA mimic protein / DNA mimicking / uracil-DNA glycosylase inhibitor / uracil-DNA glycosylase / Herpes simplex virus | |||||||||
Function / homology | Function and homology information base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / uracil DNA N-glycosylase activity / host cell nucleus / metal ion binding Similarity search - Function | |||||||||
Biological species | Human herpesvirus 1 (Herpes simplex virus type 1) Staphylococcus aureus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å | |||||||||
Authors | Wang, H.C. / Ko, T.P. / Huang, M.F. / Wang, A.H.J. | |||||||||
Funding support | Taiwan, 2items
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Citation | Journal: Nucleic Acids Res. / Year: 2016 Title: Using structural-based protein engineering to modulate the differential inhibition effects of SAUGI on human and HSV uracil DNA glycosylase. Authors: Wang, H.C. / Ho, C.H. / Chou, C.C. / Ko, T.P. / Huang, M.F. / Hsu, K.C. / Wang, A.H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ays.cif.gz | 165.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ays.ent.gz | 128.8 KB | Display | PDB format |
PDBx/mmJSON format | 5ays.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ay/5ays ftp://data.pdbj.org/pub/pdb/validation_reports/ay/5ays | HTTPS FTP |
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-Related structure data
Related structure data | 5ayrC 1lauS 3wdgS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 28922.137 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 91-334 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human herpesvirus 1 (strain 17) / Strain: 17 / Gene: UL2 / Production host: Escherichia coli (E. coli) / References: UniProt: P10186, uracil-DNA glycosylase #2: Protein | Mass: 13367.123 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q936H5 #3: 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: 2.36 Å3/Da / Density % sol: 47.85 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate pH 5.6, 30% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 19, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→20 Å / Num. obs: 41236 / % possible obs: 95.6 % / Redundancy: 2.1 % / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 4.3 / % possible all: 95.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1LAU, 3WDG Resolution: 2.09→20 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.807 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.261 / ESU R Free: 0.187 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.903 Å2
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Refinement step | Cycle: LAST / Resolution: 2.09→20 Å
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Refine LS restraints |
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