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Yorodumi- PDB-6p0g: N-terminal domain of Thermococcus Gammatolerans McrB bound to m5C DNA -
+Open data
-Basic information
Entry | Database: PDB / ID: 6p0g | ||||||
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Title | N-terminal domain of Thermococcus Gammatolerans McrB bound to m5C DNA | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / YTH domain / restriction endonuclease / DNA Binding Protein / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information endonuclease activity / ATP hydrolysis activity / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Thermococcus gammatolerans (archaea) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å | ||||||
Authors | Hosford, C.J. / Chappie, J.S. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2020 Title: The structure of theThermococcus gammatoleransMcrB N-terminal domain reveals a new mode of substrate recognition and specificity among McrB homologs. Authors: Hosford, C.J. / Bui, A.Q. / Chappie, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6p0g.cif.gz | 52.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6p0g.ent.gz | 38 KB | Display | PDB format |
PDBx/mmJSON format | 6p0g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6p0g_validation.pdf.gz | 432.3 KB | Display | wwPDB validaton report |
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Full document | 6p0g_full_validation.pdf.gz | 434 KB | Display | |
Data in XML | 6p0g_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 6p0g_validation.cif.gz | 11.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p0/6p0g ftp://data.pdbj.org/pub/pdb/validation_reports/p0/6p0g | 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: 21737.219 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus gammatolerans (strain DSM 15229 / JCM 11827 / EJ3) (archaea) Strain: DSM 15229 / JCM 11827 / EJ3 / Gene: TGAM_0453 / Variant: DSM 15229 / JCM 11827 / EJ3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C5A3Z3 |
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#2: DNA chain | Mass: 1809.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: DNA chain | Mass: 1809.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: 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: 2.5 Å3/Da / Density % sol: 50.81 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES pH 7.5, 18% PEG 3350, 0.20 M Ammonium sulfate PH range: 7.0 - 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 12, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.27→53.754 Å / Num. obs: 17710 / % possible obs: 99.4 % / Redundancy: 4.11 % / Net I/σ(I): 18 |
Reflection shell | Resolution: 2.27→2.45 Å / Redundancy: 3.85 % / Mean I/σ(I) obs: 2.59 / Num. unique obs: 2477 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.27→53.754 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 39.3
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.27→53.754 Å
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Refine LS restraints |
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LS refinement shell |
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