+Open data
-Basic information
Entry | Database: PDB / ID: 1eh6 | ||||||
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Title | HUMAN O6-ALKYLGUANINE-DNA ALKYLTRANSFERASE | ||||||
Components | O6-ALKYLGUANINE-DNA ALKYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / ALKYLTRANSFERASE / METHYLTRANSFERASE / DNA REPAIR | ||||||
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 / MAD / Resolution: 2 Å | ||||||
Authors | Daniels, D.S. / Tainer, J.A. | ||||||
Citation | Journal: EMBO J. / Year: 2000 Title: Active and alkylated human AGT structures: a novel zinc site, inhibitor and extrahelical base binding. Authors: Daniels, D.S. / Mol, C.D. / Arvai, A.S. / Kanugula, S. / Pegg, A.E. / Tainer, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1eh6.cif.gz | 48.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1eh6.ent.gz | 33.8 KB | Display | PDB format |
PDBx/mmJSON format | 1eh6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1eh6_validation.pdf.gz | 367.4 KB | Display | wwPDB validaton report |
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Full document | 1eh6_full_validation.pdf.gz | 366.9 KB | Display | |
Data in XML | 1eh6_validation.xml.gz | 4.8 KB | Display | |
Data in CIF | 1eh6_validation.cif.gz | 7.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eh/1eh6 ftp://data.pdbj.org/pub/pdb/validation_reports/eh/1eh6 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21671.949 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) References: UniProt: P16455, methylated-DNA-[protein]-cysteine S-methyltransferase |
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#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.4 % Description: INITIAL PHASES TO 3.0 ANGSTROMS CALCULATED USING 3 WAVELENGTHS OF DATA FROM A SINGLE GOLD DERIVATIVE COLLECTED AT ALS, BL 5.0.2 | |||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 18 MG/ML PROTEIN, 1.5 M SUCROSE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | |||||||||||||||
Crystal | *PLUS | |||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ | |||||||||||||||
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: SSRL / Beamline: BL9-1 / Wavelength: 0.98 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 16, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 48730 / Num. obs: 14536 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 3.298 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 6.1 / Net I/σ(I): 17.0985 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.03 % / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 3.105 / Num. unique all: 1415 / Rsym value: 36.7 / % possible all: 96.7 |
Reflection | *PLUS Num. measured all: 48730 |
Reflection shell | *PLUS % possible obs: 96.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2→19.21 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1763066.59 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: ILE 141 IS LOCATED IN A TIGHT TURN PRECEDING THE ACTIVE SITE AND CONSTRAINED IN A DISALLOWED RAMACHANDRAN REGION.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 65.68 Å2 / ksol: 0.432 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→19.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 10.2 % / Rfactor obs: 0.197 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 31.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.265 / % reflection Rfree: 10.9 % / Rfactor Rwork: 0.253 |