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Open data
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Basic information
Entry | Database: PDB / ID: 4ypr | ||||||
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Title | Crystal Structure of D144N MutY bound to its anti-substrate | ||||||
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![]() | Hydrolase/DNA / 8-oxoguanine / base-excision repair / anti-substrate / Hydrolase-DNA complex | ||||||
Function / homology | ![]() adenine glycosylase / adenine/guanine mispair binding / purine-specific mismatch base pair DNA N-glycosylase activity / DNA N-glycosylase activity / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / oxidized purine DNA binding / mismatch repair / base-excision repair / 4 iron, 4 sulfur cluster binding / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, L. / Lee, S. / Verdine, G.L. | ||||||
![]() | ![]() Title: Structural Basis for Avoidance of Promutagenic DNA Repair by MutY Adenine DNA Glycosylase. Authors: Wang, L. / Lee, S.J. / Verdine, G.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 344 KB | Display | ![]() |
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PDB format | ![]() | 277.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 489.8 KB | Display | ![]() |
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Full document | ![]() | 509.6 KB | Display | |
Data in XML | ![]() | 28.3 KB | Display | |
Data in CIF | ![]() | 39.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4yoqC ![]() 4yphC ![]() 1rrqS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 42097.941 Da / Num. of mol.: 2 / Mutation: P164C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: pET28 / Production host: ![]() ![]() References: UniProt: P83847, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds #2: DNA chain | Mass: 3300.159 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: DNA chain | Mass: 3423.249 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4 Å3/Da / Density % sol: 69.28 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.6 / Details: 100 mM Tris, pH 8.6, 1.75 M (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 13, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→117.69 Å / Num. obs: 45851 / % possible obs: 100 % / Redundancy: 5.7 % / Biso Wilson estimate: 50.22 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.054 / Net I/σ(I): 15.5 / Num. measured all: 262741 |
Reflection shell | Resolution: 2.59→2.73 Å / Redundancy: 5.8 % / Rmerge(I) obs: 1.117 / Mean I/σ(I) obs: 1.8 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1RRQ Resolution: 2.59→85.014 Å / FOM work R set: 0.818 / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.66 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 189.01 Å2 / Biso mean: 57.65 Å2 / Biso min: 23.66 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.59→85.014 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.59→2.6463 Å
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Refinement TLS params. | Method: refined / Origin x: 32.934 Å / Origin y: 41.7401 Å / Origin z: -7.7291 Å
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Refinement TLS group |
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