+Open data
-Basic information
Entry | Database: PDB / ID: 5kdw | ||||||
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Title | IMPa metallopeptidase from Pseudomonas aeruginosa | ||||||
Components | MetallopeptidaseMetalloproteinase | ||||||
Keywords | HYDROLASE / O-glycopeptidase / PF13402/M60-like | ||||||
Function / homology | Function and homology information negative regulation of leukocyte tethering or rolling / protein transport by the Sec complex / protein secretion by the type II secretion system / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / protein catabolic process / metallopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Noach, I. / Boraston, A.B. | ||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017 Title: Recognition of protein-linked glycans as a determinant of peptidase activity. Authors: Noach, I. / Ficko-Blean, E. / Pluvinage, B. / Stuart, C. / Jenkins, M.L. / Brochu, D. / Buenbrazo, N. / Wakarchuk, W. / Burke, J.E. / Gilbert, M. / Boraston, A.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kdw.cif.gz | 405.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kdw.ent.gz | 320.7 KB | Display | PDB format |
PDBx/mmJSON format | 5kdw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kd/5kdw ftp://data.pdbj.org/pub/pdb/validation_reports/kd/5kdw | HTTPS FTP |
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-Related structure data
Related structure data | 5kd2C 5kd5C 5kd8C 5kdjC 5kdnC 5kdsC 5kduC 5kdvSC 5kdxC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 96379.289 Da / Num. of mol.: 2 / Fragment: UNP residues 42-923 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) (bacteria) Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA0572 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q9I5W4 #2: Chemical | ChemComp-EDO / #3: Chemical | #4: Chemical | ChemComp-PO4 / #5: 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: 3.41 Å3/Da / Density % sol: 63.92 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: PEG 3350, NaH2PO4, Bicine pH 9 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Jul 8, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→100.09 Å / Num. obs: 219649 / % possible obs: 100 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.85→1.95 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 2.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5KDV Resolution: 1.85→100.09 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.564 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.097 / 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: 22.172 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→100.09 Å
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Refine LS restraints |
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