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- PDB-1kg5: Crystal structure of the K142Q mutant of E.coli MutY (core fragment) -
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Open data
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Basic information
Entry | Database: PDB / ID: 1kg5 | ||||||
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Title | Crystal structure of the K142Q mutant of E.coli MutY (core fragment) | ||||||
![]() | A/G-specific adenine glycosylase | ||||||
![]() | HYDROLASE / DNA Repair | ||||||
Function / homology | ![]() adenine glycosylase / adenine/guanine mispair binding / purine-specific mismatch base pair 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 / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Gilboa, R. / Kilshtein, A. / Zharkov, D.O. / Kycia, J.H. / Gerchman, S.E. / Grollman, A.P. / Shoham, G. | ||||||
![]() | ![]() Title: Analysis of the E.coli MutY DNA glycosylase structure and function by site-directed mutagenesis Authors: Gilboa, R. / Kilshtein, A. / Zharkov, D.O. / Kycia, J.H. / Gerchman, S.E. / Grollman, A.P. / Shoham, G. #1: ![]() Title: Role for Lysine 142 in the excision of adenine from A:G mispairs by MutY DNA glycosylase of Escherichia coli. Authors: Zharkov, D.O. / Gilboa, R. / Yagil, I. / Kycia, J.H. / Gerchman, S.E. / Shoham, G. / Grollmam, A.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 117.8 KB | Display | ![]() |
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PDB format | ![]() | 90 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 399.1 KB | Display | ![]() |
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Full document | ![]() | 401.4 KB | Display | |
Data in XML | ![]() | 6.4 KB | Display | |
Data in CIF | ![]() | 11.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1kg2SC ![]() 1kg3C ![]() 1kg4C ![]() 1kg6C ![]() 1kg7C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 25047.939 Da / Num. of mol.: 1 / Fragment: Catalytic domain / Mutation: K142Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P17802, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds | ||
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#2: Chemical | ChemComp-SO4 / | ||
#3: Chemical | ChemComp-SF4 / | ||
#4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.75 Å3/Da / Density % sol: 50.26 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Lithium sulfate, HEPES, Sodium chloride, Magnesium sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 16, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→40 Å / Num. all: 49330 / Num. obs: 49330 / % possible obs: 91.7 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 11.1 Å2 / Rsym value: 0.062 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.35→1.37 Å / Redundancy: 2 % / Num. unique all: 1464 / Rsym value: 0.214 / % possible all: 55.4 |
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Processing
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Refinement | Method to determine structure: Difference fourier Starting model: 1KG2 Resolution: 1.35→40 Å / Num. parameters: 19273 / Num. restraintsaints: 23153 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH & HUBER / Details: CNS 0.9 WAS ALSO USED IN REFINEMENT.
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Displacement parameters | Biso mean: 15.5 Å2 | |||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.11 Å / Num. disordered residues: 9 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2110 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→40 Å
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Refine LS restraints |
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