+Open data
-Basic information
Entry | Database: PDB / ID: 5wql | ||||||
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Title | Structure of a PDZ-protease bound to a substrate-binding adaptor | ||||||
Components |
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Keywords | PROTEIN BINDING/SIGNALING PROTEIN/HYDROLASE/PEPTIDE / Prc / NlpI / protein degradation / peptidoglycan / PROTEIN BINDING-SIGNALING PROTEIN-HYDROLASE-PEPTIDE complex | ||||||
Function / homology | Function and homology information C-terminal processing peptidase / peptidoglycan metabolic process / protein catabolic process / protein-macromolecule adaptor activity / outer membrane-bounded periplasmic space / endopeptidase activity / cell cycle / cell division / response to antibiotic / serine-type endopeptidase activity ...C-terminal processing peptidase / peptidoglycan metabolic process / protein catabolic process / protein-macromolecule adaptor activity / outer membrane-bounded periplasmic space / endopeptidase activity / cell cycle / cell division / response to antibiotic / serine-type endopeptidase activity / signal transduction / protein homodimerization activity / proteolysis / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Su, M.Y. / Chang, C.I. | ||||||
Funding support | Taiwan, 1items
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Citation | Journal: Nat Commun / Year: 2017 Title: Structural basis of adaptor-mediated protein degradation by the tail-specific PDZ-protease Prc Authors: Su, M.Y. / Som, N. / Wu, C.Y. / Su, S.C. / Kuo, Y.T. / Ke, L.C. / Ho, M.R. / Tzeng, S.R. / Teng, C.H. / Mengin-Lecreulx, D. / Reddy, M. / Chang, C.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wql.cif.gz | 388.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wql.ent.gz | 317.9 KB | Display | PDB format |
PDBx/mmJSON format | 5wql.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wq/5wql ftp://data.pdbj.org/pub/pdb/validation_reports/wq/5wql | HTTPS FTP |
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-Related structure data
-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
-Protein , 2 types, 4 molecules BACD
#1: Protein | Mass: 31865.410 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: nlpI / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0AFB1 #2: Protein | Mass: 76707.867 Da / Num. of mol.: 2 / Mutation: K477A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: prc / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P23865, C-terminal processing peptidase |
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-Protein/peptide , 3 types, 4 molecules FHEG
#3: Protein/peptide | Mass: 444.482 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) #4: Protein/peptide | | Mass: 302.326 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) #5: Protein/peptide | | Mass: 462.522 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) |
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-Non-polymers , 1 types, 946 molecules
#6: 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: 2.95 Å3/Da / Density % sol: 58.32 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 0.2 M Ammonium citrate, 14% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1.2 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: May 25, 2016 |
Radiation | Monochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→104.35 Å / Num. obs: 105941 / % possible obs: 99.9 % / Redundancy: 4.5 % / CC1/2: 0.955 / Rmerge(I) obs: 0.067 / Net I/σ(I): 21.05 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.682 / CC1/2: 0.817 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1XNF, 4QL6 Resolution: 2.3→104.35 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.893 / Cross valid method: THROUGHOUT / ESU R: 0.339 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.84 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→104.35 Å
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Refine LS restraints |
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