+Open data
-Basic information
Entry | Database: PDB / ID: 1q0s | ||||||
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Title | Binary Structure of T4DAM with AdoHcy | ||||||
Components | DNA adenine methylase | ||||||
Keywords | TRANSFERASE / T4DAM / Methyltransferase | ||||||
Function / homology | Function and homology information symbiont-mediated evasion of host restriction-modification system / DNA-methyltransferase activity / site-specific DNA-methyltransferase (adenine-specific) / site-specific DNA-methyltransferase (adenine-specific) activity / S-adenosyl-L-methionine binding / DNA restriction-modification system / mismatch repair / DNA replication / sequence-specific DNA binding / methylation ...symbiont-mediated evasion of host restriction-modification system / DNA-methyltransferase activity / site-specific DNA-methyltransferase (adenine-specific) / site-specific DNA-methyltransferase (adenine-specific) activity / S-adenosyl-L-methionine binding / DNA restriction-modification system / mismatch repair / DNA replication / sequence-specific DNA binding / methylation / symbiont-mediated suppression of host innate immune response / virus-mediated perturbation of host defense response Similarity search - Function | ||||||
Biological species | Enterobacteria phage T4 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Yang, Z. / Horton, J.R. / Zhou, L. / Zhang, X.J. / Dong, A. / Zhang, X. / Schlagman, S.L. / Kossykh, V. / Hattman, S. / Cheng, X. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2003 Title: Structure of the bacteriophage T4 DNA adenine methyltransferase Authors: Yang, Z. / Horton, J.R. / Zhou, L. / Zhang, X.J. / Dong, A. / Zhang, X. / Schlagman, S.L. / Kossykh, V. / Hattman, S. / Cheng, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1q0s.cif.gz | 63 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1q0s.ent.gz | 46 KB | Display | PDB format |
PDBx/mmJSON format | 1q0s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1q0s_validation.pdf.gz | 448.7 KB | Display | wwPDB validaton report |
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Full document | 1q0s_full_validation.pdf.gz | 455.5 KB | Display | |
Data in XML | 1q0s_validation.xml.gz | 7.2 KB | Display | |
Data in CIF | 1q0s_validation.cif.gz | 10.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q0/1q0s ftp://data.pdbj.org/pub/pdb/validation_reports/q0/1q0s | 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: 30463.805 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Gene: DAM / Plasmid: PJW2 / Production host: Escherichia coli (E. coli) References: UniProt: P04392, site-specific DNA-methyltransferase (adenine-specific) |
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#2: Chemical | ChemComp-SAH / |
#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: 2.21 Å3/Da / Density % sol: 44.23 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6 Details: Ammonium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 16 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 13015 / Num. obs: 12701 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 2.35→2.37 Å / Rmerge(I) obs: 0.229 / Mean I/σ(I) obs: 3.9 / % possible all: 99.6 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 56092 |
Reflection shell | *PLUS % possible obs: 99.6 % |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→18 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.3→18 Å
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Refine LS restraints |
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Xplor file |
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Refinement | *PLUS | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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