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Yorodumi- 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 | ||||||
Components |
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Keywords | DNA BINDING / MISMATCH RECOGNITION / ATP-BINDING | ||||||
| Function / homology | Function and homology informationadenine/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 | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Natrajan, G. / Lamers, M.H. / Enzlin, J.H. / Winterwerp, H.H.K. / Perrakis, A. / Sixma, T.K. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2003Title: 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: Journal: Nature / Year: 2000Title: 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. | ||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 1oh8.cif.gz | 325.4 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb1oh8.ent.gz | 259 KB | Display | PDB format |
| PDBx/mmJSON format | 1oh8.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 1oh8_validation.pdf.gz | 805.4 KB | Display | wwPDB validaton report |
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| Full document | 1oh8_full_validation.pdf.gz | 838.4 KB | Display | |
| Data in XML | 1oh8_validation.xml.gz | 55.5 KB | Display | |
| Data in CIF | 1oh8_validation.cif.gz | 76.2 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oh/1oh8 ftp://data.pdbj.org/pub/pdb/validation_reports/oh/1oh8 | HTTPS FTP |
-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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| 1 |
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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 




| #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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934 |
| 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: MOLECULAR REPLACEMENTStarting 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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