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Yorodumi- PDB-4fmo: Structure of the C-terminal domain of the Saccharomyces cerevisia... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fmo | ||||||
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Title | Structure of the C-terminal domain of the Saccharomyces cerevisiae MUTL alpha (MLH1/PMS1) heterodimer bound to a fragment of exo1 | ||||||
Components |
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Keywords | HYDROLASE / Mismatch repair / MUTL / endonuclease / Zn-binding protein / DNA damage / DNA repair | ||||||
Function / homology | Function and homology information gene conversion at mating-type locus => GO:0007534 / meiotic heteroduplex formation / MutLbeta complex / MutLgamma complex / meiotic DNA double-strand break processing / telomeric 3' overhang formation / MutLalpha complex / flap endonuclease activity / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / meiotic mismatch repair ...gene conversion at mating-type locus => GO:0007534 / meiotic heteroduplex formation / MutLbeta complex / MutLgamma complex / meiotic DNA double-strand break processing / telomeric 3' overhang formation / MutLalpha complex / flap endonuclease activity / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / meiotic mismatch repair / 5'-flap endonuclease activity / mismatched DNA binding / DNA double-strand break processing / mitotic G2/M transition checkpoint / reciprocal meiotic recombination / 5'-3' exonuclease activity / 5'-3' DNA exonuclease activity / ATP-dependent DNA damage sensor activity / mismatch repair / telomere maintenance / DNA recombination / Hydrolases; Acting on ester bonds / ATP hydrolysis activity / mitochondrion / DNA binding / ATP binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.04 Å | ||||||
Authors | Gueneau, E. / Legrand, P. / Charbonnier, J.B. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2013 Title: Structure of the MutL alpha C-terminal domain reveals how Mlh1 contributes to Pms1 endonuclease site. Authors: Gueneau, E. / Dherin, C. / Legrand, P. / Tellier-Lebegue, C. / Gilquin, B. / Bonnesoeur, P. / Londino, F. / Quemener, C. / Le Du, M.H. / Marquez, J.A. / Moutiez, M. / Gondry, M. / Boiteux, S. / Charbonnier, J.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fmo.cif.gz | 212.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fmo.ent.gz | 170.5 KB | Display | PDB format |
PDBx/mmJSON format | 4fmo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4fmo_validation.pdf.gz | 442.8 KB | Display | wwPDB validaton report |
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Full document | 4fmo_full_validation.pdf.gz | 448.1 KB | Display | |
Data in XML | 4fmo_validation.xml.gz | 19.2 KB | Display | |
Data in CIF | 4fmo_validation.cif.gz | 26 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fm/4fmo ftp://data.pdbj.org/pub/pdb/validation_reports/fm/4fmo | HTTPS FTP |
-Related structure data
Related structure data | 4e4wSC 4fmnC C: citing same article (ref.) S: Starting model for refinement |
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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
-DNA mismatch repair protein ... , 2 types, 2 molecules AB
#1: Protein | Mass: 33239.102 Da / Num. of mol.: 1 / Fragment: UNP residues 483-769 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: MLH1, PMS2, YMR167W, YM8520.16 / Production host: Escherichia coli (E. coli) / References: UniProt: P38920 |
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#2: Protein | Mass: 27948.195 Da / Num. of mol.: 1 / Fragment: UNP residues 635-873 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: PMS1, YNL082W, N2317 / Production host: Escherichia coli (E. coli) / References: UniProt: P14242 |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 1030.201 Da / Num. of mol.: 1 / Fragment: UNP residues 443-450 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P39875 |
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-Non-polymers , 3 types, 59 molecules
#4: Chemical | ChemComp-MG / | ||
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#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.83 Å3/Da / Density % sol: 67.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: PEG, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 24, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 3.04→50 Å / Num. all: 18310 / Num. obs: 18219 / % possible obs: 99.5 % / Redundancy: 5.6 % / Biso Wilson estimate: 70.27 Å2 / Rmerge(I) obs: 0.136 / Net I/σ(I): 10 |
Reflection shell | Resolution: 3.04→3.23 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.793 / Mean I/σ(I) obs: 2.2 / % possible all: 98.1 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4E4W Resolution: 3.04→48.41 Å / Cor.coef. Fo:Fc: 0.9304 / Cor.coef. Fo:Fc free: 0.9301 / SU R Cruickshank DPI: 0.691 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 98.37 Å2
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Refine analyze | Luzzati coordinate error obs: 0.687 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.04→48.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.04→3.22 Å / Total num. of bins used: 9
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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