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Yorodumi- PDB-6njv: C-terminal region of the Xanthomonas campestris pv. campestris OL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6njv | ||||||
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Title | C-terminal region of the Xanthomonas campestris pv. campestris OLD protein phased with iodine | ||||||
Components | Xcc_CTR_I | ||||||
Keywords | UNKNOWN FUNCTION / Nuclease / Toprim | ||||||
Function / homology | Overcoming lysogenization defect protein-like, TOPRIM domain / OLD protein-like, TOPRIM domain / AAA domain, group 15 / AAA ATPase domain / P-loop containing nucleoside triphosphate hydrolase / metal ion binding / IODIDE ION / Uncharacterized protein Function and homology information | ||||||
Biological species | Xanthomonas campestris pv. campestris (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å | ||||||
Authors | Schiltz, C.J. / Lee, A. / Partlow, E.A. / Hosford, C.J. / Chappie, J.S. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2019 Title: Structural characterization of Class 2 OLD family nucleases supports a two-metal catalysis mechanism for cleavage. Authors: Schiltz, C.J. / Lee, A. / Partlow, E.A. / Hosford, C.J. / 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 | 6njv.cif.gz | 65.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6njv.ent.gz | 38.4 KB | Display | PDB format |
PDBx/mmJSON format | 6njv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6njv_validation.pdf.gz | 425.6 KB | Display | wwPDB validaton report |
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Full document | 6njv_full_validation.pdf.gz | 427 KB | Display | |
Data in XML | 6njv_validation.xml.gz | 10.2 KB | Display | |
Data in CIF | 6njv_validation.cif.gz | 12.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nj/6njv ftp://data.pdbj.org/pub/pdb/validation_reports/nj/6njv | 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: 26036.361 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xanthomonas campestris pv. campestris (strain B100) (bacteria) Strain: B100 / Gene: XCCB100_2436 / Production host: Escherichia coli (E. coli) / References: UniProt: B0RTN2 | ||||
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#2: Chemical | #3: Chemical | ChemComp-MG / | #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: 2.52 Å3/Da / Density % sol: 51.26 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M Bis Tris Propane pH 7.0-8.0, 11-26% PEG 3350, 0.15-0.2 M sodium iodide, and 0.25 M NDSB-195 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.6531 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 3, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.6531 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→64.39 Å / Num. obs: 29501 / % possible obs: 99.39 % / Redundancy: 6.7 % / Biso Wilson estimate: 50.89 Å2 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 1.99→2.04 Å |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.3→64.39 Å / SU ML: 0.3121 / Cross valid method: FREE R-VALUE / σ(F): 1.84 / Phase error: 31.7308 / Stereochemistry target values: GeoStd + Monomer Library
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.47 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→64.39 Å
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Refine LS restraints |
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LS refinement shell |
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