+Open data
-Basic information
Entry | Database: PDB / ID: 1eh8 | ||||||
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Title | BENZYLATED 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 / Resolution: 2.5 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 | 1eh8.cif.gz | 48.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1eh8.ent.gz | 32.5 KB | Display | PDB format |
PDBx/mmJSON format | 1eh8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1eh8_validation.pdf.gz | 377 KB | Display | wwPDB validaton report |
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Full document | 1eh8_full_validation.pdf.gz | 378.1 KB | Display | |
Data in XML | 1eh8_validation.xml.gz | 5.5 KB | Display | |
Data in CIF | 1eh8_validation.cif.gz | 7.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eh/1eh8 ftp://data.pdbj.org/pub/pdb/validation_reports/eh/1eh8 | HTTPS FTP |
-Related structure data
Related structure data | 1eh6SC 1eh7C S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 21762.072 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: CYS 145 HAS BEEN ALKYLATED BY REACTION WITH O6-BENZYLGUANINE 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: 2.58 Å3/Da / Density % sol: 52.39 % | |||||||||||||||
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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 298K | |||||||||||||||
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: BL7-1 / Wavelength: 1.08 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 25, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. all: 17635 / Num. obs: 8007 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 2.023 % / Biso Wilson estimate: 27.5 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 8.9409 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 2.221 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 1.927 / % possible all: 98.7 |
Reflection | *PLUS Highest resolution: 2.5 Å / Num. measured all: 17635 |
Reflection shell | *PLUS % possible obs: 98.7 % |
-Processing
Software |
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Refinement | Starting model: PDB 1EH6 Resolution: 2.5→19.95 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1323183 / 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: 54.94 Å2 / ksol: 0.43 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→19.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.026 / 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: 10.6 % / Rfactor obs: 0.194 / Rfactor Rfree: 0.23 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 35.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.286 / % reflection Rfree: 9.7 % / Rfactor Rwork: 0.255 |