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Open data
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Basic information
Entry | Database: PDB / ID: 5kdu | |||||||||
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Title | ZmpB metallopeptidase in complex with a2,6-Sialyl T-antigen | |||||||||
![]() | F5/8 type C domain protein | |||||||||
![]() | HYDROLASE / Glycopeptidase / O-glycan / PF13402 | |||||||||
Function / homology | ![]() hydrolase activity, acting on glycosyl bonds / metabolic process / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Noach, I. / Ficko-Blean, E. / Stuart, C. / 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 | ![]() | 134.6 KB | Display | ![]() |
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PDB format | ![]() | 99.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 782.7 KB | Display | ![]() |
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Full document | ![]() | 784.8 KB | Display | |
Data in XML | ![]() | 25.4 KB | Display | |
Data in CIF | ![]() | 38.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5kd2C ![]() 5kd5C ![]() 5kd8C ![]() 5kdjSC ![]() 5kdnC ![]() 5kdsC ![]() 5kdvC ![]() 5kdwC ![]() 5kdxC 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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Unit cell |
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Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 60080.852 Da / Num. of mol.: 1 / Fragment: UNP residues 497-1003 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A Gene: CPF_1489 Production host: ![]() ![]() References: UniProt: A0A0H2YN38 |
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#2: Polysaccharide | beta-D-galactopyranose-(1-3)-[N-acetyl-alpha-neuraminic acid-(2-6)]2-acetamido-2-deoxy-alpha-D-galactopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 4 types, 500 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/SER.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/SER.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-ZN / | #5: Chemical | ChemComp-SER / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.22 Å3/Da / Density % sol: 61.76 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 3350, Na/K tartrate, HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: May 27, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 2→85.47 Å / Num. obs: 53306 / % possible obs: 100 % / Redundancy: 6.3 % / CC1/2: 0.992 / Rmerge(I) obs: 0.131 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 3 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5KDJ Resolution: 2→85.47 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 4.702 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.125 / 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: 33.106 Å2
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Refinement step | Cycle: LAST / Resolution: 2→85.47 Å
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Refine LS restraints |
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