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Open data
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Basic information
Entry | Database: PDB / ID: 5kdv | ||||||
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Title | IMPa metallopeptidase from Pseudomonas aeruginosa | ||||||
![]() | Metallopeptidase | ||||||
![]() | HYDROLASE / O-glycopeptidase / PF13402/M60-like | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Noach, I. / Boraston, A.B. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 201.3 KB | Display | ![]() |
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PDB format | ![]() | 162.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451 KB | Display | ![]() |
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Full document | ![]() | 453.1 KB | Display | |
Data in XML | ![]() | 38.8 KB | Display | |
Data in CIF | ![]() | 59.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5kd2C ![]() 5kd5C ![]() 5kd8C ![]() 5kdjC ![]() 5kdnC ![]() 5kdsC ![]() 5kduC ![]() 5kdwC ![]() 5kdxC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 97159.109 Da / Num. of mol.: 1 / Fragment: UNP residues 42-923 / Mutation: Y766N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA0572 Production host: ![]() ![]() References: UniProt: Q9I5W4 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-ZN / | #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.53 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: PEG 3350, (NH4)2SO4, Bicine pH 9.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Mar 9, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→48.72 Å / Num. obs: 90627 / % possible obs: 98.8 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.93→2.03 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 4.2 / % possible all: 97.9 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.704 Å2
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Refinement step | Cycle: 1 / Resolution: 1.93→48.72 Å
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Refine LS restraints |
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