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Open data
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Basic information
Entry | Database: PDB / ID: 5kd8 | |||||||||
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Title | BT_4244 metallopeptidase in complex with Tn antigen. | |||||||||
![]() | Metallopeptidase | |||||||||
![]() | HYDROLASE / O-glycopeptidase / PF13402/M60-like / O-glycan / Hydrolase. | |||||||||
Function / homology | ![]() positive regulation of protein targeting to membrane / transmembrane transporter binding / metal ion binding / plasma membrane 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 | ![]() | 131.2 KB | Display | ![]() |
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PDB format | ![]() | 97.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 465.4 KB | Display | ![]() |
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Full document | ![]() | 467.8 KB | Display | |
Data in XML | ![]() | 22 KB | Display | |
Data in CIF | ![]() | 31.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5kd2SC ![]() 5kd5C ![]() 5kdjC ![]() 5kdnC ![]() 5kdsC ![]() 5kduC ![]() 5kdvC ![]() 5kdwC ![]() 5kdxC S: Starting model for refinement 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
-Protein / Sugars , 2 types, 2 molecules A![](data/chem/img/A2G.gif)
![](data/chem/img/A2G.gif)
#1: Protein | Mass: 64272.113 Da / Num. of mol.: 1 / Fragment: UNP residues 322-857 Source method: isolated from a genetically manipulated source Details: In complex with Tn antigen Source: (gene. exp.) ![]() Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_4244 Production host: ![]() ![]() References: UniProt: Q89ZX7 |
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#6: Sugar | ChemComp-A2G / |
-Non-polymers , 5 types, 161 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/SER.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/SER.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / | ||||||
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#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-SER / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.46 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG 3350, NaH2PO4, Tris-HCl pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Oct 8, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→43.72 Å / Num. obs: 34533 / % possible obs: 99.9 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 3.3 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5KD2 Resolution: 2.3→43.72 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / SU B: 7.565 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R: 0.26 / ESU R Free: 0.211 / 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: 55.519 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→43.72 Å
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Refine LS restraints |
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