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- PDB-1oh8: THE CRYSTAL STRUCTURE OF E. COLI MUTS BINDING TO DNA WITH AN UNPA... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1oh8 | ||||||
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Title | THE CRYSTAL STRUCTURE OF E. COLI MUTS BINDING TO DNA WITH AN UNPAIRED THYMIDINE | ||||||
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![]() | DNA BINDING / MISMATCH RECOGNITION / ATP-BINDING | ||||||
Function / homology | ![]() adenine/cytosine mispair binding / MutS complex / mismatch repair complex / regulation of DNA recombination / mismatched DNA binding / DNA binding, bending / ATP-dependent DNA damage sensor activity / mismatch repair / ADP binding / damaged DNA binding ...adenine/cytosine mispair binding / MutS complex / mismatch repair complex / regulation of DNA recombination / mismatched DNA binding / DNA binding, bending / ATP-dependent DNA damage sensor activity / mismatch repair / ADP binding / damaged DNA binding / DNA damage response / ATP hydrolysis activity / ATP binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Natrajan, G. / Lamers, M.H. / Enzlin, J.H. / Winterwerp, H.H.K. / Perrakis, A. / Sixma, T.K. | ||||||
![]() | ![]() Title: Structures of E. Coli DNA Mismatch Repair Enzyme Muts in Complex with Different Mismatches: A Common Recognition Mode for Diverse Substrates Authors: Natrajan, G. / Lamers, M.H. / Enzlin, J.H. / Winterwerp, H.H.K. / Perrakis, A. / Sixma, T.K. #1: ![]() Title: The Crystal Structure of DNA Mismatch Repair Protein Muts Binding to a G X T Mismatch Authors: Lamers, M.H. / Perrakis, A. / Enzlin, J.H. / Winterwerp, H.H. / De Wind, N. / Sixma, T.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 325.4 KB | Display | ![]() |
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PDB format | ![]() | 259 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1oh5C ![]() 1oh6C ![]() 1oh7C ![]() 1e3mS 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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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 89604.359 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-800 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-DNA chain , 2 types, 2 molecules EF
#2: DNA chain | Mass: 9184.905 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / Source: (synth.) synthetic construct (others) |
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#3: DNA chain | Mass: 9569.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 139 molecules ![](data/chem/img/ADP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-ADP / |
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#5: Chemical | ChemComp-MG / |
#6: Water | ChemComp-HOH / |
-Details
Compound details | THIS PROTEIN IS INVOLVED IN THE REPAIR OF MISMATCHES IN DNA. IT CARRIES OUT THE MISMATCH ...THIS PROTEIN IS INVOLVED IN THE REPAIR OF MISMATCHES |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.2 % Description: STRUCTURE DETERMINED BY RIGID BODY REFINEMENT USING REFMAC5 | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 Details: 12-14 % PEG 6000, 150-300 MM NACL 25 MM HEPES PH 7-8, 10 MM MGCL2, 100-150 MICROM ADP | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 15, 2001 / Details: MIRRORS |
Radiation | Monochromator: GE 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→25 Å / Num. obs: 47871 / % possible obs: 98.3 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 9.54 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.725 / Mean I/σ(I) obs: 2.2 / % possible all: 92.4 |
Reflection | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 15 Å / Num. obs: 48882 / Num. measured all: 332212 / Rmerge(I) obs: 0.124 |
Reflection shell | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 3 Å / % possible obs: 92.4 % / Rmerge(I) obs: 0.725 / Mean I/σ(I) obs: 1.57 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1E3M Resolution: 2.9→15 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.867 / SU B: 20.82 / SU ML: 0.38 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.464 / 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: 21.05 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→15 Å
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Refine LS restraints |
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