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Yorodumi- PDB-1oh7: THE CRYSTAL STRUCTURE OF E. COLI MUTS BINDING TO DNA WITH A G:G M... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1oh7 | ||||||
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Title | THE CRYSTAL STRUCTURE OF E. COLI MUTS BINDING TO DNA WITH A G:G MISMATCH | ||||||
Components |
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Keywords | DNA BINDING / MISMATCH RECOGNITION | ||||||
Function / homology | Function and homology information 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 | ESCHERICHIA COLI (E. coli) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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: 2003 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: Journal: Nature / Year: 2000 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1oh7.cif.gz | 329.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oh7.ent.gz | 262.8 KB | Display | PDB format |
PDBx/mmJSON format | 1oh7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1oh7_validation.pdf.gz | 823.7 KB | Display | wwPDB validaton report |
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Full document | 1oh7_full_validation.pdf.gz | 854.9 KB | Display | |
Data in XML | 1oh7_validation.xml.gz | 54.2 KB | Display | |
Data in CIF | 1oh7_validation.cif.gz | 75.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oh/1oh7 ftp://data.pdbj.org/pub/pdb/validation_reports/oh/1oh7 | HTTPS FTP |
-Related structure data
Related structure data | 1oh5C 1oh6C 1oh8C 1e3mS S: Starting model for refinement C: citing same article (ref.) |
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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, 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.) ESCHERICHIA COLI (E. coli) / Strain: B834 DE3 / Variant: PLYSS / Plasmid: PM800 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 DE3 / Variant (production host): PLYSS / References: UniProt: P23909 |
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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: 9304.978 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 91 molecules
#4: Chemical | ChemComp-ADP / |
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#5: Chemical | ChemComp-MG / |
#6: Water | ChemComp-HOH / |
-Details
Compound details | FUNCTION: THIS PROTEIN IS INVOLVED IN THE REPAIR OF MISMATCHES IN DNA. IT CARRIES OUT THE MISMATCH ...FUNCTION: 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: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 15, 2002 / Details: MIRRORS |
Radiation | Monochromator: GE220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→40 Å / Num. obs: 68892 / % possible obs: 91.2 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.628 / Mean I/σ(I) obs: 1.08 / % possible all: 60.5 |
Reflection | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 15 Å / Num. obs: 75563 / Num. measured all: 382803 / Rmerge(I) obs: 0.104 |
Reflection shell | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 2.7 Å / % possible obs: 60.5 % / Rmerge(I) obs: 0.628 / Mean I/σ(I) obs: 1.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1E3M Resolution: 2.5→15 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.912 / SU B: 13.4 / SU ML: 0.276 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.551 / ESU R Free: 0.315 / 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: 20.8 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→15 Å
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Refine LS restraints |
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