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Yorodumi- PDB-6p8s: Structure of P. aeruginosa ATCC27853 HORMA1:HORMA2:Peptide 1 complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 6p8s | ||||||
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Title | Structure of P. aeruginosa ATCC27853 HORMA1:HORMA2:Peptide 1 complex | ||||||
Components |
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Keywords | PROTEIN BINDING / HORMA domain / closure motif / CD-NTase / cGAS | ||||||
Function / homology | Bacterial HORMA domain / Bacterial HORMA domain 2 / HORMA domain superfamily / defense response to virus / ACETATE ION / Transcriptional regulator / CD-NTase-associated protein 8 / CD-NTase-associated protein 7 / HORMA domain containing protein Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 | 6p8s.cif.gz | 357.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6p8s.ent.gz | 295.5 KB | Display | PDB format |
PDBx/mmJSON format | 6p8s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p8/6p8s ftp://data.pdbj.org/pub/pdb/validation_reports/p8/6p8s | HTTPS FTP |
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-Related structure data
Related structure data | 6p80C 6p82C 6p8jC 6p8oC 6p8pSC 6p8rSC 6p8uC 6p8vC 6pb3C 6u7bC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data set type: diffraction image data / Metadata reference: 10.15785/SBGRID/678 |
-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 on special symmetry positions |
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-Components
-Protein , 2 types, 4 molecules ABCD
#1: Protein | Mass: 18723.082 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) Gene: ORF C60, CAZ10_14260, DY940_15620, DY979_07580, EGY23_20890, EQH76_12140, IPC669_24875, PA5486_02901, PAERUG_E15_London_28_01_14_04350, PAMH19_6113 Production host: Escherichia coli (E. coli) / References: UniProt: Q8GQ50, UniProt: P0DTF6*PLUS #2: Protein | Mass: 14411.179 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) Gene: DY979_07575, EGY23_20885, IPC669_24870, PA5486_02900, PAERUG_E15_London_28_01_14_04349 Production host: Escherichia coli (E. coli) / References: UniProt: A0A0F6RRN7, UniProt: P0DTF5*PLUS |
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-Protein/peptide , 1 types, 2 molecules EF
#3: Protein/peptide | Mass: 1137.219 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli (E. coli) |
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-Non-polymers , 4 types, 514 molecules
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-1PE / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 2.5 Å3/Da / Density % sol: 50.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 mM HEPES pH 7.5, 0.5 M Sodium acetate, 31% PEG 3350, and 1 mM ATP |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 28, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2→39.2 Å / Num. obs: 44741 / % possible obs: 96 % / Redundancy: 9.6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.219 / Rpim(I) all: 0.074 / Rrim(I) all: 0.232 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.878 / Mean I/σ(I) obs: 1 / Num. unique obs: 2481 / CC1/2: 0.521 / Rpim(I) all: 0.787 / Rrim(I) all: 2.043 / % possible all: 73.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6P8P, 6P8R Resolution: 2→39.197 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.6
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→39.197 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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