[English] 日本語
![](img/lk-miru.gif)
- PDB-4fmn: Structure of the C-terminal domain of the Saccharomyces cerevisia... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4fmn | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the C-terminal domain of the Saccharomyces cerevisiae MUTL alpha (MLH1/PMS1) heterodimer bound to a fragment of NTG2 | ||||||
![]() |
| ||||||
![]() | HYDROLASE / Mismatch repair / MUTL / endonuclease / Zn-binding protein / DNA damage / DNA repair | ||||||
Function / homology | ![]() Cleavage of the damaged pyrimidine / : / meiotic heteroduplex formation / MutLbeta complex / MutLgamma complex / MutLalpha complex / oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / meiotic mismatch repair / base-excision repair, AP site formation ...Cleavage of the damaged pyrimidine / : / meiotic heteroduplex formation / MutLbeta complex / MutLgamma complex / MutLalpha complex / oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / meiotic mismatch repair / base-excision repair, AP site formation / mismatched DNA binding / reciprocal meiotic recombination / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / ATP-dependent DNA damage sensor activity / mismatch repair / DNA-(apurinic or apyrimidinic site) endonuclease activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / base-excision repair / 4 iron, 4 sulfur cluster binding / ATP hydrolysis activity / mitochondrion / DNA binding / ATP binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gueneau, E. / Legrand, P. / Charbonnier, J.B. | ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 121 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 91.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 468.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 476.9 KB | Display | |
Data in XML | ![]() | 21 KB | Display | |
Data in CIF | ![]() | 29.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4e4wSC ![]() 4fmoC C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
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.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: MLH1, PMS2, YMR167W, YM8520.16 / Production host: ![]() ![]() |
---|---|
#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.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: PMS1, YNL082W, N2317 / Production host: ![]() ![]() |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 1085.342 Da / Num. of mol.: 1 / Fragment: UNP residues 22-29 / Source method: obtained synthetically / Details: Synthetic peptide / Source: (synth.) ![]() ![]() |
---|
-Non-polymers , 4 types, 144 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-EDO / #6: Chemical | #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.77 Å3/Da / Density % sol: 67.34 % |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
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: 2.69→50 Å / Num. all: 25931 / Num. obs: 25750 / % possible obs: 99.3 % / Redundancy: 5.6 % / Biso Wilson estimate: 66.07 Å2 / Rsym value: 0.098 |
Reflection shell | Resolution: 2.69→2.86 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.768 / % possible all: 96.8 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4E4W Resolution: 2.69→31.63 Å / Cor.coef. Fo:Fc: 0.9421 / Cor.coef. Fo:Fc free: 0.9315 / SU R Cruickshank DPI: 0.304 / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 85.23 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.398 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.69→31.63 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.69→2.8 Å / Total num. of bins used: 13
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|