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Yorodumi- PDB-5xe9: Crystal Structure of the Complex of the Peptidase Domain of Strep... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xe9 | ||||||
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Title | Crystal Structure of the Complex of the Peptidase Domain of Streptococcus mutans ComA with a Small Molecule Inhibitor. | ||||||
Components | Putative ABC transporter, ATP-binding protein ComA | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / peptidase / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information single-species submerged biofilm formation / ABC-type bacteriocin transporter activity / ATPase-coupled lipid transmembrane transporter activity / cysteine-type peptidase activity / ATP hydrolysis activity / proteolysis / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Streptococcus mutans serotype c (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.101 Å | ||||||
Authors | Ishii, S. / Fukui, K. / Yokoshima, S. / Kumagai, K. / Beniyama, Y. / Kodama, T. / Fukuyama, T. / Okabe, T. / Nagano, T. / Kojima, H. / Yano, T. | ||||||
Citation | Journal: Sci Rep / Year: 2017 Title: High-throughput Screening of Small Molecule Inhibitors of the Streptococcus Quorum-sensing Signal Pathway Authors: Ishii, S. / Fukui, K. / Yokoshima, S. / Kumagai, K. / Beniyama, Y. / Kodama, T. / Fukuyama, T. / Okabe, T. / Nagano, T. / Kojima, H. / Yano, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xe9.cif.gz | 121.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xe9.ent.gz | 93.4 KB | Display | PDB format |
PDBx/mmJSON format | 5xe9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xe/5xe9 ftp://data.pdbj.org/pub/pdb/validation_reports/xe/5xe9 | HTTPS FTP |
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-Related structure data
Related structure data | 5xe8C 3k8uS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17353.826 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The first methionine and the last 15 residues are not identified in the crystal structure. Source: (gene. exp.) Streptococcus mutans serotype c (bacteria) Strain: ATCC 700610 / UA159 / Gene: SMU_286 / Plasmid: pET-21b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: Q8DW05 #2: Chemical | ChemComp-6CH / [( | #3: 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: 2.47 Å3/Da / Density % sol: 50.18 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 100mM ammonium sulfate, 50mM bis-tris, 12.5%(w/v) polyethylene glycol 3,350. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jun 28, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. obs: 6568 / % possible obs: 95.6 % / Redundancy: 6.3 % / Net I/σ(I): 26.8 |
Reflection shell | Resolution: 3.1→3.21 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.177 / Mean I/σ(I) obs: 17.5 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3K8U Resolution: 3.101→31.575 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.88
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.101→31.575 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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