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- PDB-1v0e: Endosialidase of Bacteriophage K1F -

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Basic information

Entry
Database: PDB / ID: 1v0e
TitleEndosialidase of Bacteriophage K1F
ComponentsENDO-ALPHA-SIALIDASE
KeywordsHYDROLASE / 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 / metabolic process / virion attachment to host cell / identical protein binding
Similarity search - Function
Endosialidase, N-terminal extension domain / Endosialidase, beta barrel domain / Endosialidase, C-terminal domain superfamily / Endosialidase, domain 4 / Endosialidase, domain 4 / Glycosyl hydrolase 58 / Endosialidase, beta propeller domain / Endosialidase, N-terminal extension domain / Endosialidase, C-terminal domain / Beta barrel domain of bacteriophage endosialidase ...Endosialidase, N-terminal extension domain / Endosialidase, beta barrel domain / Endosialidase, C-terminal domain superfamily / Endosialidase, domain 4 / Endosialidase, domain 4 / Glycosyl hydrolase 58 / Endosialidase, beta propeller domain / Endosialidase, N-terminal extension domain / Endosialidase, C-terminal domain / Beta barrel domain of bacteriophage endosialidase / Catalytic beta propeller domain of bacteriophage endosialidase / N terminal extension of bacteriophage endosialidase / Catalytic domain of bacteriophage endosialidase / Tail spike TSP1/Gp66, N-terminal domain / Tail spike TSP1/Gp66 receptor binding N-terminal domain / Chaperone of endosialidase / Intramolecular chaperone auto-processing domain / Intramolecular chaperone auto-processing (ICA) domain profile. / Bacteriophage T7 tail fibre protein / Phage T7 tail fibre protein / Transcription Regulator spoIIAA / Elongation Factor Tu (Ef-tu); domain 3 - #20 / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / ATP synthase subunit alpha, N-terminal domain-like superfamily / Elongation Factor Tu (Ef-tu); domain 3 / Few Secondary Structures / Irregular / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Tail spike protein / Tail spike protein
Similarity search - Component
Biological speciesCOLIPHAGE K1F (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsStummeyer, 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
DepositionMar 28, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2004Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_special_symmetry / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENDO-ALPHA-SIALIDASE
B: ENDO-ALPHA-SIALIDASE
C: ENDO-ALPHA-SIALIDASE
D: ENDO-ALPHA-SIALIDASE
E: ENDO-ALPHA-SIALIDASE
F: ENDO-ALPHA-SIALIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)445,36212
Polymers444,7926
Non-polymers5706
Water55,3963075
1
A: ENDO-ALPHA-SIALIDASE
B: ENDO-ALPHA-SIALIDASE
C: ENDO-ALPHA-SIALIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,6816
Polymers222,3963
Non-polymers2853
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
D: ENDO-ALPHA-SIALIDASE
E: ENDO-ALPHA-SIALIDASE
F: ENDO-ALPHA-SIALIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,6816
Polymers222,3963
Non-polymers2853
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)99.650, 131.250, 346.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11B-2286-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.499, -0.449, -0.741), (0.461, 0.586, -0.666), (0.734, -0.674, -0.085)108.354, 26.356, 43.794
2given(-0.505, 0.46, 0.73), (-0.444, 0.587, -0.677), (-0.74, -0.666, -0.092)10.295, 62.355, 101.973
3given(-1, 0.01, -0.004), (-0.009, -0.957, -0.291), (-0.007, -0.291, 0.957)24.217, 21.699, 3.787
4given(0.504, -0.453, -0.735), (0.648, -0.365, 0.669), (-0.571, -0.813, 0.109)14.102, -68.066, 82.808
5given(0.499, 0.458, 0.736), (-0.653, -0.36, 0.666), (0.57, -0.813, 0.119)-83.985, -16.947, 37.302

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Components

#1: Protein
ENDO-ALPHA-SIALIDASE / ENDOSIALIDASE


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: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3075 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.21 %
Crystal growpH: 7.5 / Details: pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.8416
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8416 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 335241 / % possible obs: 93.7 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.103
Reflection shellRmerge(I) obs: 0.352 / % possible all: 96

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.9→30 Å / SU B: 3.163 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.131
RfactorNum. reflection% reflectionSelection details
Rfree0.20228 16879 5 %RANDOM
Rwork0.16597 ---
obs0.16781 318265 93.7 %-
Displacement parametersBiso mean: 15.374 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20 Å20 Å2
2---0.57 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31380 0 30 3075 34485

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