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Yorodumi- PDB-5kds: ZmpB metallopeptidase in complex with an O-glycopeptide (a2,6-sia... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kds | |||||||||
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Title | ZmpB metallopeptidase in complex with an O-glycopeptide (a2,6-sialylated core-3 pentapeptide). | |||||||||
Components |
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Keywords | HYDROLASE / O-glycopeptidase / PF13402/M60-like / Bovine submaxillary mucin / O-glycan | |||||||||
Function / homology | Function and homology information hydrolase activity, acting on glycosyl bonds / metabolic process / metal ion binding Similarity search - Function | |||||||||
Biological species | Clostridium perfringens (bacteria) Bos taurus (cattle) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | |||||||||
Authors | Noach, I. / Ficko-Blean, E. / Stuart, C. / 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 | 5kds.cif.gz | 145.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kds.ent.gz | 106.4 KB | Display | PDB format |
PDBx/mmJSON format | 5kds.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kd/5kds ftp://data.pdbj.org/pub/pdb/validation_reports/kd/5kds | HTTPS FTP |
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-Related structure data
Related structure data | 5kd2C 5kd5C 5kd8C 5kdjSC 5kdnC 5kduC 5kdvC 5kdwC 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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1 |
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Unit cell |
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-Components
-Protein/peptide / Protein / Sugars , 3 types, 3 molecules GA
#1: Protein/peptide | Mass: 401.415 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Glycopeptide fragment derived from bovine submaxillary mucin Source: (natural) Bos taurus (cattle) |
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#2: Protein | Mass: 60080.852 Da / Num. of mol.: 1 / Fragment: UNP residues 497-1003 Source method: isolated from a genetically manipulated source Details: In complex with a BSM fragment. Source: (gene. exp.) Clostridium perfringens (strain ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A) (bacteria) Strain: ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A Gene: CPF_1489 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A0H2YN38 |
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-[N-acetyl-alpha-neuraminic acid-(2-6)]2-acetamido-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(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 , 5 types, 802 molecules
#4: Chemical | ChemComp-ZN / | ||
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#5: Chemical | ChemComp-TLA / | ||
#6: Chemical | ChemComp-EPE / | ||
#7: Chemical | ChemComp-EDO / #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.55 % |
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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: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 28, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→40 Å / Num. obs: 99964 / % possible obs: 96 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 20.9 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 4.6 / % possible all: 76 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5KDJ Resolution: 1.6→40 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.259 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.071 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 22.982 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→40 Å
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Refine LS restraints |
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