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- PDB-6p8s: Structure of P. aeruginosa ATCC27853 HORMA1:HORMA2:Peptide 1 complex -
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Open data
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Basic information
Entry | Database: PDB / ID: 6p8s | ||||||
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Title | Structure of P. aeruginosa ATCC27853 HORMA1:HORMA2:Peptide 1 complex | ||||||
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![]() | 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![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ye, Q. / Corbett, K.D. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 357.4 KB | Display | ![]() |
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PDB format | ![]() | 295.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 492.1 KB | Display | ![]() |
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Full document | ![]() | 495.7 KB | Display | |
Data in XML | ![]() | 28.5 KB | Display | |
Data in CIF | ![]() | 42.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-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 ( |
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Similar structure data | |
Experimental dataset #1 | Data set type: diffraction image data / Metadata reference: 10.15785/SBGRID/678 |
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Links
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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.) ![]() ![]() 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: ![]() ![]() #2: Protein | Mass: 14411.179 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: DY979_07575, EGY23_20885, IPC669_24870, PA5486_02900, PAERUG_E15_London_28_01_14_04349 Production host: ![]() ![]() |
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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.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 4 types, 514 molecules ![](data/chem/img/ACT.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/HOH.gif)
#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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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