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Yorodumi- PDB-7rqh: Crystal Structure of carboxyl-terminal processing protease A muta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7rqh | ||||||
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Title | Crystal Structure of carboxyl-terminal processing protease A mutant S302A, CtpA_S302A, of Pseudomonas aeruginosa | ||||||
Components | Probable carboxyl-terminal protease | ||||||
Keywords | HYDROLASE / CtpA / CTP | ||||||
Function / homology | Function and homology information cell envelope organization / cell envelope / cell wall biogenesis / protein secretion by the type III secretion system / outer membrane-bounded periplasmic space / endopeptidase activity / periplasmic space / serine-type endopeptidase activity / signal transduction / proteolysis / plasma membrane Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Hsu, H.C. / Li, H. | ||||||
Funding support | United States, 1items
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Citation | Journal: Mbio / Year: 2022 Title: Pseudomonas aeruginosa C-Terminal Processing Protease CtpA Assembles into a Hexameric Structure That Requires Activation by a Spiral-Shaped Lipoprotein-Binding Partner. Authors: Hsu, H.C. / Wang, M. / Kovach, A. / Darwin, A.J. / Li, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7rqh.cif.gz | 114.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rqh.ent.gz | 85.5 KB | Display | PDB format |
PDBx/mmJSON format | 7rqh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7rqh_validation.pdf.gz | 438 KB | Display | wwPDB validaton report |
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Full document | 7rqh_full_validation.pdf.gz | 445.2 KB | Display | |
Data in XML | 7rqh_validation.xml.gz | 19.5 KB | Display | |
Data in CIF | 7rqh_validation.cif.gz | 25.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rq/7rqh ftp://data.pdbj.org/pub/pdb/validation_reports/rq/7rqh | HTTPS FTP |
-Related structure data
Related structure data | 7rpqSC 7rqfC S: Starting model for refinement C: citing same article (ref.) |
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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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Unit cell |
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-Components
#1: Protein | Mass: 42806.336 Da / Num. of mol.: 2 / Mutation: S302A 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: PA5134 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9HU50 |
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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: 5.3 Å3/Da / Density % sol: 76.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 0.1 M sodium acetate, pH 4.0, and 0.6 M ammonium dihydrogen phosphate at a concentration of 33 mg/mL PH range: 4.0 -4.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.07803 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 16, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07803 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→94.82 Å / Num. obs: 28884 / % possible obs: 99.6 % / Redundancy: 10.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 3.2→3.37 Å / Redundancy: 10.6 % / Num. unique obs: 4245 / CC1/2: 0.524 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7RPQ Resolution: 3.2→43.03 Å / SU ML: 0.61 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 32.32 / 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: 3.2→43.03 Å
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Refine LS restraints |
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LS refinement shell |
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