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Open data
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Basic information
Entry | Database: PDB / ID: 5kdx | |||||||||
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Title | IMPa metallopeptidase in complex with T-antigen | |||||||||
![]() | Metallopeptidase | |||||||||
![]() | HYDROLASE / O-glycopeptidase / PF13402/M60-like / core-1 O-glycan | |||||||||
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 | ![]() | 382.6 KB | Display | ![]() |
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PDB format | ![]() | 301.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 73.1 KB | Display | |
Data in CIF | ![]() | 109.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5kd2C ![]() 5kd5C ![]() 5kd8C ![]() 5kdjC ![]() 5kdnC ![]() 5kdsC ![]() 5kduC ![]() 5kdvSC ![]() 5kdwC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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 / Sugars , 2 types, 4 molecules AB
#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.) ![]() Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA0572 Production host: ![]() ![]() References: UniProt: Q9I5W4 #2: Polysaccharide | |
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-Non-polymers , 5 types, 1348 molecules ![](data/chem/img/PO4.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/SER.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/SER.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-PO4 / #4: Chemical | #5: Chemical | ChemComp-EDO / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.47 Å3/Da / Density % sol: 64.54 % |
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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: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: May 28, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→48.12 Å / Num. obs: 102258 / % possible obs: 99.6 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 2.3 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5KDV Resolution: 2.4→48.12 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.86 / SU B: 8.243 / SU ML: 0.183 / Cross valid method: THROUGHOUT / ESU R: 0.314 / ESU R Free: 0.245 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.42 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→48.12 Å
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Refine LS restraints |
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