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Yorodumi- PDB-1e3m: The crystal structure of E. coli MutS binding to DNA with a G:T m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1e3m | ||||||
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Title | The crystal structure of E. coli MutS binding to DNA with a G:T 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) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å | ||||||
Authors | Lamers, M.H. / Perrakis, A. / Enzlin, J.H. / Winterwerp, H.H.K. / De Wind, N. / Sixma, T.K. | ||||||
Citation | 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.K. / 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 | 1e3m.cif.gz | 333.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e3m.ent.gz | 279.3 KB | Display | PDB format |
PDBx/mmJSON format | 1e3m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1e3m_validation.pdf.gz | 797.6 KB | Display | wwPDB validaton report |
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Full document | 1e3m_full_validation.pdf.gz | 835 KB | Display | |
Data in XML | 1e3m_validation.xml.gz | 61.4 KB | Display | |
Data in CIF | 1e3m_validation.cif.gz | 86.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e3/1e3m ftp://data.pdbj.org/pub/pdb/validation_reports/e3/1e3m | HTTPS FTP |
-Related structure data
Similar structure data |
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-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: 90729.859 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-800 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Cellular location: NUCLEUS / Gene: MUTS / Cellular location (production host): CYTOPLASM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / 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: DNA OLIGONUCLEOTIDES, ANNEALED / Source: (synth.) ESCHERICHIA COLI (E. coli) |
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#3: DNA chain | Mass: 9279.964 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA OLIGONUCLEOTIDES, ANNEALED / Source: (synth.) ESCHERICHIA COLI (E. coli) |
-Non-polymers , 3 types, 481 molecules
#4: Chemical | ChemComp-ADP / | ||
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#5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Compound details | FUNCTION: THIS PROTEIN IS INVOLVED IN THE REPAIR OF MISMATCHES IN DNA. IT IS POSSIBLE THAT IT CARRY ...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: 2.7 Å3/Da / Density % sol: 55 % / Description: MAD DATA WERE COLLECTED IN ESRF BM14 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 Details: 12-14 % PEG 6000, 150-300 MM NACL, 100 MM HEPES PH 7-8, 10 MM MGCL2, 100-150 MICROM ADP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop / Details: used microseeding | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 0.933 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 15, 2000 |
Radiation | Monochromator: SI111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. obs: 109670 / % possible obs: 98.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 2.2 / % possible all: 95.1 |
Reflection shell | *PLUS % possible obs: 95.1 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.2→20 Å / SU B: 7.181 / SU ML: 0.183 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.253 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Displacement parameters | Biso mean: 46.62 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Software | *PLUS Name: REFMAC / Version: 5 / Classification: refinement | ||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.22891 / Rfactor Rfree: 0.26613 / Rfactor Rwork: 0.22814 | ||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 46.622 Å2 | ||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.367 / Rfactor obs: 0.324 |