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Yorodumi- PDB-4rtl: Complex of Escherichia coli DNA Adenine Methyltransferase (DAM) w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rtl | ||||||
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Title | Complex of Escherichia coli DNA Adenine Methyltransferase (DAM) with Sinefungin and with DNA Containing Distal Pap Regulon Sequence | ||||||
Components |
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Keywords | Transferase/DNA / DAM METHYLATION / GATC RECOGNITION / BASE FLIPPING / BACTERIAL VIRULENCE / methylation-independent transcriptional repressor / Transferase-DNA complex | ||||||
Function / homology | Function and homology information bacterial-type DNA replication initiation / site-specific DNA-methyltransferase (adenine-specific) / site-specific DNA-methyltransferase (adenine-specific) activity / S-adenosyl-L-methionine binding / DNA restriction-modification system / mismatch repair / response to UV / DNA-templated DNA replication / methylation / sequence-specific DNA binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.193 Å | ||||||
Authors | Horton, J.R. / Cheng, X. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rtl.cif.gz | 147.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rtl.ent.gz | 112.1 KB | Display | PDB format |
PDBx/mmJSON format | 4rtl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4rtl_validation.pdf.gz | 706.7 KB | Display | wwPDB validaton report |
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Full document | 4rtl_full_validation.pdf.gz | 708.2 KB | Display | |
Data in XML | 4rtl_validation.xml.gz | 13 KB | Display | |
Data in CIF | 4rtl_validation.cif.gz | 17.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rt/4rtl ftp://data.pdbj.org/pub/pdb/validation_reports/rt/4rtl | HTTPS FTP |
-Related structure data
Related structure data | 4rtjC 4rtkC 4rtmC 4rtnC 4rtoC 4rtpC 4rtqC 4rtrC 4rtsC 2g1pS 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: 34330.961 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 substr. MDS42 / Gene: dam, ECMDS42_2833 / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3) / References: UniProt: H0Q7C9, UniProt: P0AEE8*PLUS |
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#2: DNA chain | Mass: 3357.223 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: DNA chain | Mass: 3348.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: Chemical | ChemComp-SFG / |
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.77 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 24% PEG200, 100mM KCl, 10mM MgSO4, 100mM MES buffer, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 15, 2006 |
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: 2.19→27.606 Å / Num. all: 20122 / Num. obs: 20122 / % possible obs: 99.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 8.7 % / Biso Wilson estimate: 39.2 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 24.4 |
Reflection shell | Resolution: 2.19→2.27 Å / Redundancy: 7 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 5.7 / Num. unique all: 1955 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2G1P Resolution: 2.193→27.6 Å / SU ML: 0.3 / σ(F): 1.33 / Phase error: 27.24 / 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: 2.193→27.6 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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