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Yorodumi- PDB-7tvh: Hyperlytic variant of Tae1, Type VI secretion amidase effector 1,... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7tvh | ||||||
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Title | Hyperlytic variant of Tae1, Type VI secretion amidase effector 1, from Pseudomonas aeruginosa (Cys110Ser) | ||||||
Components | Peptidoglycan amidase Tse1 | ||||||
Keywords | HYDROLASE / Type VI secretion amidase effector / Tae1 Hyperlytic variant / Cys110Ser / ANTIMICROBIAL PROTEIN | ||||||
Function / homology | gamma-D-glutamyl-meso-diaminopimelate peptidase / amidase activity / host cell membrane / Papain-like cysteine peptidase superfamily / extracellular region / membrane / Peptidoglycan amidase Tse1 Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å | ||||||
Authors | Radkov, A. / Saunders, H. / Chou, S. | ||||||
Funding support | United States, 1items
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Citation | Journal: Elife / Year: 2022 Title: Antibacterial potency of type VI amidase effector toxins is dependent on substrate topology and cellular context. Authors: Radkov, A. / Sapiro, A.L. / Flores, S. / Henderson, C. / Saunders, H. / Kim, R. / Massa, S. / Thompson, S. / Mateusiak, C. / Biboy, J. / Zhao, Z. / Starita, L.M. / Hatleberg, W.L. / Vollmer, ...Authors: Radkov, A. / Sapiro, A.L. / Flores, S. / Henderson, C. / Saunders, H. / Kim, R. / Massa, S. / Thompson, S. / Mateusiak, C. / Biboy, J. / Zhao, Z. / Starita, L.M. / Hatleberg, W.L. / Vollmer, W. / Russell, A.B. / Simorre, J.P. / Anthony-Cahill, S. / Brzovic, P. / Hayes, B. / Chou, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7tvh.cif.gz | 154.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tvh.ent.gz | 98 KB | Display | PDB format |
PDBx/mmJSON format | 7tvh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7tvh_validation.pdf.gz | 453.8 KB | Display | wwPDB validaton report |
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Full document | 7tvh_full_validation.pdf.gz | 457 KB | Display | |
Data in XML | 7tvh_validation.xml.gz | 25.6 KB | Display | |
Data in CIF | 7tvh_validation.cif.gz | 36.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tv/7tvh ftp://data.pdbj.org/pub/pdb/validation_reports/tv/7tvh | HTTPS FTP |
-Related structure data
Related structure data | 4eobS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 17513.762 Da / Num. of mol.: 4 / Mutation: C110S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: tse1, PA1844 / Production host: Escherichia coli (E. coli) References: UniProt: Q9I2Q1, gamma-D-glutamyl-meso-diaminopimelate peptidase #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: 2.49 Å3/Da / Density % sol: 50.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2 M sodium thiocyanate 0.1 M HEPES pH 7.5 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 91 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.97954 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 23, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97954 Å / Relative weight: 1 |
Reflection | Resolution: 1.71→82.27 Å / Num. obs: 72921 / % possible obs: 98.45 % / Redundancy: 2 % / Biso Wilson estimate: 26.46 Å2 / CC1/2: 0.999 / Net I/σ(I): 10.48 |
Reflection shell | Resolution: 1.71→1.771 Å / Rmerge(I) obs: 0.9019 / Num. unique obs: 6437 / CC1/2: 0.469 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4EOB Resolution: 1.71→82.27 Å / SU ML: 0.2619 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.4055 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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: 38.61 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.71→82.27 Å
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Refine LS restraints |
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LS refinement shell |
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