+Open data
-Basic information
Entry | Database: PDB / ID: 6pb3 | ||||||
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Title | Structure of Rhizobiales Trip13 | ||||||
Components | Rhizobiales Sp. Pch2 | ||||||
Keywords | PROTEIN BINDING / ATPase / Remodeller / HORMA domain / TRIP13 / Pch2 | ||||||
Function / homology | ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / ATP hydrolysis activity / P-loop containing nucleoside triphosphate hydrolase / ATP binding / ATPase associated with various cellular activities family protein Function and homology information | ||||||
Biological species | MARINE METAGENOME (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.048 Å | ||||||
Authors | Ye, Q. / Corbett, K.D. | ||||||
Citation | Journal: Mol.Cell / Year: 2020 Title: HORMA Domain Proteins and a Trip13-like ATPase Regulate Bacterial cGAS-like Enzymes to Mediate Bacteriophage Immunity. Authors: Ye, Q. / Lau, R.K. / Mathews, I.T. / Birkholz, E.A. / Watrous, J.D. / Azimi, C.S. / Pogliano, J. / Jain, M. / Corbett, K.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6pb3.cif.gz | 111 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pb3.ent.gz | 89.4 KB | Display | PDB format |
PDBx/mmJSON format | 6pb3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pb/6pb3 ftp://data.pdbj.org/pub/pdb/validation_reports/pb/6pb3 | HTTPS FTP |
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-Related structure data
Related structure data | 6p80C 6p82C 6p8jC 6p8oC 6p8pC 6p8rC 6p8sC 6p8uC 6p8vC 6u7bC C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.15785/SBGRID/681 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33710.297 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MARINE METAGENOME (others) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1B3NHK7*PLUS |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 100 mM sodium citrate pH 6.0, 1.6 M NH2SO4, and 0.2 M sodium/potassium tartrate |
-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: 0.9792 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 11, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.048→86.98 Å / Num. obs: 17737 / % possible obs: 99.3 % / Redundancy: 10.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.019 / Rrim(I) all: 0.061 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 2.05→2.1 Å / Redundancy: 10.2 % / Rmerge(I) obs: 1.955 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1347 / CC1/2: 0.54 / Rpim(I) all: 0.635 / Rrim(I) all: 2.057 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.048→86.98 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 0.33 / Phase error: 32.49 / 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: 2.048→86.98 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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