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Yorodumi- PDB-1v0f: Endosialidase of Bacteriophage K1F in complex with oligomeric alp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1v0f | |||||||||
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Title | Endosialidase of Bacteriophage K1F in complex with oligomeric alpha-2,8-sialic acid | |||||||||
Components | ENDO-ALPHA-SIALIDASE | |||||||||
Keywords | HYDROLASE / ENDOSIALIDASE / POLYSIALIC ACID DEGRADATION / GLYCOSIDASE. | |||||||||
Function / homology | Function and homology information endo-alpha-sialidase / endo-alpha-(2,8)-sialidase activity / symbiont entry into host cell via disruption of host cell glycocalyx / virus tail, fiber / symbiont entry into host cell via disruption of host cell envelope / symbiont entry into host / adhesion receptor-mediated virion attachment to host cell / virion attachment to host cell / identical protein binding Similarity search - Function | |||||||||
Biological species | COLIPHAGE K1F (virus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.55 Å | |||||||||
Authors | Stummeyer, K. / Dickmanns, A. / Muehlenhoff, M. / Gerady-Schahn, R. / Ficner, R. | |||||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2005 Title: Crystal Structure of the Polysialic Acid-Degrading Endosialidase of Bacteriophage K1F Authors: Stummeyer, K. / Dickmanns, A. / Muehlenhoff, M. / Gerardy-Schahn, R. / Ficner, R. #1: Journal: J.Biol.Chem. / Year: 2003 Title: Proteolytic Processing and Oligomerization of Bacteriophage-Derived Endosialidases Authors: Muhlenhoff, M. / Stummeyer, K. / Grove, M. / Sauerborn, M. / Gerardy-Schahn, R. | |||||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1v0f.cif.gz | 759.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1v0f.ent.gz | 628.4 KB | Display | PDB format |
PDBx/mmJSON format | 1v0f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1v0f_validation.pdf.gz | 3.2 MB | Display | wwPDB validaton report |
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Full document | 1v0f_full_validation.pdf.gz | 3.3 MB | Display | |
Data in XML | 1v0f_validation.xml.gz | 149.6 KB | Display | |
Data in CIF | 1v0f_validation.cif.gz | 204.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v0/1v0f ftp://data.pdbj.org/pub/pdb/validation_reports/v0/1v0f | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 74131.969 Da / Num. of mol.: 6 / Fragment: CATALYTIC DOMAIN, RESIDUES 246-911 Source method: isolated from a genetically manipulated source Source: (gene. exp.) COLIPHAGE K1F (virus) / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: Q858B1, UniProt: Q04830*PLUS, endo-alpha-sialidase #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-SLB / #4: Chemical | ChemComp-PO4 / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.65 % |
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Crystal grow | pH: 7.5 / Details: pH 7.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9195 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9195 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→30 Å / Num. obs: 130540 / % possible obs: 88.4 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 2.55→2.7 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 2.4 / % possible all: 79.8 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 2.55→30 Å / SU B: 10.739 / SU ML: 0.231 / Cross valid method: THROUGHOUT / ESU R Free: 0.321
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Displacement parameters | Biso mean: 21.406 Å2
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Refinement step | Cycle: LAST / Resolution: 2.55→30 Å
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