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- PDB-4rtr: Complex of Escherichia coli DNA Adenine Methyltransferase (DAM) w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4rtr | ||||||
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Title | Complex of Escherichia coli DNA Adenine Methyltransferase (DAM) with AdoMet and a 5-bp non-canonical site (GTTTA ) | ||||||
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![]() | Transferase/DNA / DAM METHYLATION / GATC RECOGNITION / BASE FLIPPING / BACTERIAL VIRULENCE / methylation-independent transcriptional repressor / Transferase-DNA complex | ||||||
Function / homology | ![]() bacterial-type DNA replication initiation / macromolecule modification / site-specific DNA-methyltransferase (adenine-specific) / site-specific DNA-methyltransferase (adenine-specific) activity / S-adenosyl-L-methionine binding / mismatch repair / response to UV / DNA-templated DNA replication / methylation / sequence-specific DNA binding Similarity search - Function | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Horton, J.R. / Cheng, X. | ||||||
![]() | ![]() Title: Structures of Escherichia coli DNA adenine methyltransferase (Dam) in complex with a non-GATC sequence: potential implications for methylation-independent transcriptional repression. Authors: Horton, J.R. / Zhang, X. / Blumenthal, R.M. / Cheng, X. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 144.7 KB | Display | ![]() |
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PDB format | ![]() | 109.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 736.9 KB | Display | ![]() |
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Full document | ![]() | 737.9 KB | Display | |
Data in XML | ![]() | 12.8 KB | Display | |
Data in CIF | ![]() | 17.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4rtjC ![]() 4rtkC ![]() 4rtlC ![]() 4rtmC ![]() 4rtnC ![]() 4rtoC ![]() 4rtpC ![]() 4rtqC ![]() 4rtsC ![]() 2g1pS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34330.961 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: DNA chain | Mass: 3629.418 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: DNA chain | Mass: 3691.438 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: Chemical | ChemComp-SAM / |
#5: Water | ChemComp-HOH / |
Sequence details | AUTHOR STATES THAT RESIDUES 175 WERE MODELED AS SER INSTEAD OF ALA BECAUSE OF EXTRA DENSITY. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.26 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 30% PEG 4000, 80mM Magnesium acetate, 50mM sodium cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 14, 2007 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.39→30 Å / Num. all: 14421 / Num. obs: 14421 / % possible obs: 93.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 35.1 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2.39→2.48 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 3.8 / Num. unique all: 1360 / % possible all: 90.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2G1P Resolution: 2.393→29.959 Å / SU ML: 0.13 / σ(F): 1.36 / Phase error: 21.78 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.393→29.959 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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