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Yorodumi- PDB-3ju4: Crystal Structure Analysis of EndosialidaseNF at 0.98 A Resolution -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ju4 | ||||||
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Title | Crystal Structure Analysis of EndosialidaseNF at 0.98 A Resolution | ||||||
Components | Endo-N-acetylneuraminidase | ||||||
Keywords | HYDROLASE / endoNF / polySia / high-resolution / 1A / 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 / metabolic process / adhesion receptor-mediated virion attachment to host cell / virion attachment to host cell / identical protein binding Similarity search - Function | ||||||
Biological species | Enterobacteria phage K1F (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.98 Å | ||||||
Authors | Schulz, E.C. / Neuman, P. / Gerardy-Schahn, R. / Sheldrick, G.M. / Ficner, R. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2010 Title: Structure analysis of endosialidase NF at 0.98 A resolution. Authors: Schulz, E.C. / Neumann, P. / Gerardy-Schahn, R. / Sheldrick, G.M. / Ficner, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ju4.cif.gz | 356.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ju4.ent.gz | 284 KB | Display | PDB format |
PDBx/mmJSON format | 3ju4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ju4_validation.pdf.gz | 779.3 KB | Display | wwPDB validaton report |
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Full document | 3ju4_full_validation.pdf.gz | 787.8 KB | Display | |
Data in XML | 3ju4_validation.xml.gz | 43.1 KB | Display | |
Data in CIF | 3ju4_validation.cif.gz | 72.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ju/3ju4 ftp://data.pdbj.org/pub/pdb/validation_reports/ju/3ju4 | HTTPS FTP |
-Related structure data
Related structure data | 1v0eS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 74542.461 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 246-910 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage K1F (virus) / Strain: K1 / Plasmid: pet22b+ / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / References: UniProt: Q04830, endo-alpha-sialidase | ||||||
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#2: Sugar | ChemComp-SLB / | ||||||
#3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | Sequence details | THE DEPOSITORS | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.21 Å3/Da / Density % sol: 61.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.2 Details: 16% (w/v) PEG 8000, 0.1M Tris/HCl pH 7.2, 3% Isopropanol, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 20, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 0.98→20 Å / Num. obs: 516832 / % possible obs: 96.9 % / Redundancy: 3.3 % / Rsym value: 0.073 / Net I/σ(I): 12.41 |
Reflection shell | Resolution: 0.98→1.08 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 3.42 / Num. unique all: 429843 / Rsym value: 0.415 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1V0E Resolution: 0.98→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze | Num. disordered residues: 43 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.98→20 Å
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