[English] 日本語
Yorodumi- PDB-1yfh: wt Human O6-Alkylguanine-DNA Alkyltransferase Bound To DNA Contai... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yfh | ||||||
---|---|---|---|---|---|---|---|
Title | wt Human O6-Alkylguanine-DNA Alkyltransferase Bound To DNA Containing an Alkylated Cytosine | ||||||
Components |
| ||||||
Keywords | TRANSFERASE/DNA / protein-DNA complex / TRANSFERASE-DNA COMPLEX | ||||||
Function / homology | Function and homology information MGMT-mediated DNA damage reversal / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / DNA-methyltransferase activity / DNA ligation / DNA alkylation repair / positive regulation of double-strand break repair / methyltransferase activity / methylation / DNA repair ...MGMT-mediated DNA damage reversal / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / DNA-methyltransferase activity / DNA ligation / DNA alkylation repair / positive regulation of double-strand break repair / methyltransferase activity / methylation / DNA repair / negative regulation of apoptotic process / DNA binding / nucleoplasm / membrane / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å | ||||||
Authors | Duguid, E.M. / Rice, P.A. / He, C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: The structure of the human AGT protein bound to DNA and its implications for damage detection. Authors: Duguid, E.M. / Rice, P.A. / He, C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1yfh.cif.gz | 126.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1yfh.ent.gz | 95.8 KB | Display | PDB format |
PDBx/mmJSON format | 1yfh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yfh_validation.pdf.gz | 475.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1yfh_full_validation.pdf.gz | 500.2 KB | Display | |
Data in XML | 1yfh_validation.xml.gz | 23.3 KB | Display | |
Data in CIF | 1yfh_validation.cif.gz | 32 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yf/1yfh ftp://data.pdbj.org/pub/pdb/validation_reports/yf/1yfh | HTTPS FTP |
-Related structure data
Related structure data | 1t38S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
| ||||||||
Details | The DNA bound to monomer B is completed by two fold axis -x +1, y +.5, -z +2. |
-Components
#1: DNA chain | Mass: 5144.413 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: oligonucleotide synthesized by automated phosphoramidite technique containing unatural base #2: DNA chain | Mass: 4756.123 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: oligonucleotide synthesized by automated phosphoramidite technique #3: Protein | Mass: 19233.285 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MGMT / Plasmid: pGEX-6P-2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: P16455, methylated-DNA-[protein]-cysteine S-methyltransferase #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.64 Å3/Da / Density % sol: 66 % | ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.7 Details: PEG 4000, sodium chloride, citrate, magnesium chloride, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
|
-Data collection
Diffraction | Mean temperature: 200 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 4, 2004 / Details: Bent conical Si-mirror (Rh coating) |
Radiation | Monochromator: bent Ge (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. all: 19770 / Num. obs: 19448 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 3→3.09 Å / % possible all: 98.2 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1T38 Resolution: 3.01→29.17 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 628363.49 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 26.7255 Å2 / ksol: 0.311532 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 76.7 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.01→29.17 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 3.01→3.19 Å / Rfactor Rfree error: 0.049 / Total num. of bins used: 6
| |||||||||||||||||||||||||
Xplor file |
|