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Yorodumi- PDB-1oh5: THE CRYSTAL STRUCTURE OF E. COLI MUTS BINDING TO DNA WITH A C:A M... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1oh5 | ||||||
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Title | THE CRYSTAL STRUCTURE OF E. COLI MUTS BINDING TO DNA WITH A C:A 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: 2.9 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: 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 | 1oh5.cif.gz | 327.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oh5.ent.gz | 261 KB | Display | PDB format |
PDBx/mmJSON format | 1oh5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1oh5_validation.pdf.gz | 766.9 KB | Display | wwPDB validaton report |
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Full document | 1oh5_full_validation.pdf.gz | 795.2 KB | Display | |
Data in XML | 1oh5_validation.xml.gz | 53.7 KB | Display | |
Data in CIF | 1oh5_validation.cif.gz | 74 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oh/1oh5 ftp://data.pdbj.org/pub/pdb/validation_reports/oh/1oh5 | HTTPS FTP |
-Related structure data
Related structure data | 1oh6C 1oh7C 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: 9144.881 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: 9288.979 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 59 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: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.811 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 15, 2002 / Details: MIRRORS |
Radiation | Monochromator: TRIANGULAR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.811 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→20 Å / Num. obs: 45607 / % possible obs: 93.8 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 12.21 |
Reflection shell | Resolution: 2.9→3.03 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 1.97 / % possible all: 95.4 |
Reflection | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 15 Å / Num. obs: 48834 / % possible obs: 95.4 % / Num. measured all: 454107 / Rmerge(I) obs: 0.095 |
Reflection shell | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 3 Å / % possible obs: 93.8 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 1.97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1E3M Resolution: 2.9→15 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.886 / SU B: 19.64 / SU ML: 0.368 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.486 / 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: 37.77 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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