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Yorodumi- PDB-6u7t: MutY adenine glycosylase bound to DNA containing a transition sta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6u7t | ||||||||||||
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Title | MutY adenine glycosylase bound to DNA containing a transition state analog (1N) paired with d(8-oxo-G) | ||||||||||||
Components |
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Keywords | hydrolase/DNA / Protein-DNA complex / DNA repair / transition state analog / hydrolase-DNA complex / HYDROLASE | ||||||||||||
Function / homology | Function and homology information adenine glycosylase / purine-specific mismatch base pair DNA N-glycosylase activity / DNA N-glycosylase activity / base-excision repair / 4 iron, 4 sulfur cluster binding / DNA binding / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Geobacillus stearothermophilus (bacteria) synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||||||||
Authors | O'Shea Murray, V.L. / Cao, S. / Horvath, M.P. / David, S.S. | ||||||||||||
Funding support | United States, 2items
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Citation | Journal: Acs Chem.Biol. / Year: 2020 Title: Structural Basis for Finding OG Lesions and Avoiding Undamaged G by the DNA Glycosylase MutY. Authors: Russelburg, L.P. / O'Shea Murray, V.L. / Demir, M. / Knutsen, K.R. / Sehgal, S.L. / Cao, S. / David, S.S. / Horvath, M.P. #1: Journal: Nucleic Acids Res. / Year: 2016 Title: Structure and stereochemistry of the base excision repair glycosylase MutY reveal a mechanism similar to retaining glycosidases. Authors: Woods, R.D. / O'Shea, V.L. / Chu, A. / Cao, S. / Richards, J.L. / Horvath, M.P. / David, S.S. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6u7t.cif.gz | 165.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6u7t.ent.gz | 125.3 KB | Display | PDB format |
PDBx/mmJSON format | 6u7t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u7/6u7t ftp://data.pdbj.org/pub/pdb/validation_reports/u7/6u7t | HTTPS FTP |
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-Related structure data
Related structure data | 6q0cC 1rrqS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 41810.629 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Gene: mutY / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P83847, adenine glycosylase |
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-DNA chain , 2 types, 2 molecules BC
#2: DNA chain | Mass: 3423.249 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#3: DNA chain | Mass: 3191.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 78 molecules
#4: Chemical | ChemComp-SF4 / | ||
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#5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 2.49 Å3/Da / Density % sol: 50.54 % Description: Dark golden-brown rod 75 micrometer x 350 micrometer |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: MICRO-SEEDED, 0.5 M CALCIUM ACETATE, 0.1 M TRIS, 14% W/V PEG4000, 0.005 M BETA-MERCAPTOETHANOL, 5% W/V ETHYLENE GLYCOL Temp details: Ambient |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.1158 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 3, 2008 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.1158 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→41.334 Å / Num. obs: 30197 / % possible obs: 94.1 % / Redundancy: 6.523 % / Biso Wilson estimate: 41.487 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Rrim(I) all: 0.09 / Χ2: 1.022 / Net I/σ(I): 15.5 / Num. measured all: 196963 / Scaling rejects: 116 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RRQ Resolution: 2→41.334 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.6
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 123.89 Å2 / Biso mean: 49.0743 Å2 / Biso min: 14.75 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→41.334 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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