+Open data
-Basic information
Entry | Database: PDB / ID: 6c5d | ||||||
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Title | N-terminal domain of Helicobacter pylori LlaJI.R1 | ||||||
Components | LlaJI.R1 | ||||||
Keywords | DNA BINDING PROTEIN / B3 domain / restriction endonuclease | ||||||
Function / homology | ATPase, dynein-related, AAA domain / AAA domain (dynein-related subfamily) / ATP hydrolysis activity / P-loop containing nucleoside triphosphate hydrolase / ATP binding / Putative restriction enzyme Function and homology information | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å | ||||||
Authors | Hosford, C.J. / Chappie, J.S. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2018 Title: The crystal structure of theHelicobacter pyloriLlaJI.R1 N-terminal domain provides a model for site-specific DNA binding. Authors: 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 | 6c5d.cif.gz | 114.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6c5d.ent.gz | 94.7 KB | Display | PDB format |
PDBx/mmJSON format | 6c5d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c5/6c5d ftp://data.pdbj.org/pub/pdb/validation_reports/c5/6c5d | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 17006.238 Da / Num. of mol.: 4 / Fragment: N-terminal domain (UNP residues 1-137) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: J99 / ATCC 700824 / Gene: jhp_0164 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9ZMQ4 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.77 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MMT, pH 6.5, 25% v/v PEG1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 21, 2017 |
Radiation | Monochromator: Cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→83.97 Å / Num. obs: 152937 / % possible obs: 93.6 % / Redundancy: 3.68 % / CC1/2: 0.997 / Rrim(I) all: 0.096 / Net I/σ(I): 9 |
Reflection shell | Resolution: 1.97→2.1 Å / Redundancy: 1.91 % / Mean I/σ(I) obs: 1.56 / Num. unique obs: 23180 / CC1/2: 0.709 / Rrim(I) all: 0.624 / % possible all: 90.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→83.97 Å / Cross valid method: FREE R-VALUE /
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Refinement step | Cycle: LAST / Resolution: 1.97→83.97 Å
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