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Yorodumi- PDB-1wb9: Crystal Structure of E. coli DNA Mismatch Repair enzyme MutS, E38... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wb9 | ||||||
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Title | Crystal Structure of E. coli DNA Mismatch Repair enzyme MutS, E38T mutant, in complex with a G.T mismatch | ||||||
Components |
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Keywords | DNA-BINDING / ATP-BINDING / DNA BINDING / DNA REPAIR / 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) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Natrajan, G. / Georgijevic, D. / Lebbink, J.H.G. / Winterwerp, H.H.K. / de Wind, N. / Sixma, T.K. | ||||||
Citation | Journal: Embo J. / Year: 2006 Title: Dual Role of Muts Glutamate 38 in DNA Mismatch Discrimination and in the Authorization of Repair. Authors: Lebbink, J.H.G. / Georgijevic, D. / Natrajan, G. / Fish, A. / Winterwerp, H.H.K. / Sixma, T.K. / De Wind, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wb9.cif.gz | 351.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wb9.ent.gz | 279.9 KB | Display | PDB format |
PDBx/mmJSON format | 1wb9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1wb9_validation.pdf.gz | 814.2 KB | Display | wwPDB validaton report |
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Full document | 1wb9_full_validation.pdf.gz | 839.9 KB | Display | |
Data in XML | 1wb9_validation.xml.gz | 64.6 KB | Display | |
Data in CIF | 1wb9_validation.cif.gz | 94.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wb/1wb9 ftp://data.pdbj.org/pub/pdb/validation_reports/wb/1wb9 | HTTPS FTP |
-Related structure data
Related structure data | 1wbbC 1wbdC 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: 89576.352 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-800 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PM800 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 (BL21) / Variant (production host): PLYSS / References: UniProt: P23909 |
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-DNA chain , 2 types, 2 molecules EF
#2: DNA chain | Mass: 5526.581 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: G\:T MISMATCH DNA |
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#3: DNA chain | Mass: 5234.382 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ESCHERICHIA COLI (E. coli) |
-Non-polymers , 3 types, 957 molecules
#4: Chemical | ChemComp-ADP / |
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#5: Chemical | ChemComp-MG / |
#6: Water | ChemComp-HOH / |
-Details
Compound details | ENGINEERED |
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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: 56.2 % |
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Crystal grow | pH: 7.5 Details: 25 MM HEPES(7.5), 300 MM NACL, 10 MM MGCL2, 14 % PEG 6000., pH 7.50 |
-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: Mar 1, 2002 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: DIAMOND (111) 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: 2.1→25 Å / Num. obs: 121248 / % possible obs: 91.7 % / Redundancy: 3.05 % / Biso Wilson estimate: 31.65 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.46 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 1.88 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.52 / % possible all: 47 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1E3M Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.927 / SU B: 5.398 / SU ML: 0.137 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.178 / 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: BABINET MODEL PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.14 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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