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- PDB-1v0f: Endosialidase of Bacteriophage K1F in complex with oligomeric alp... -

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Basic information

Entry
Database: PDB / ID: 1v0f
TitleEndosialidase of Bacteriophage K1F in complex with oligomeric alpha-2,8-sialic acid
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 / N-acetyl-beta-neuraminic acid / Tail spike protein / Tail spike protein
Similarity search - Component
Biological speciesCOLIPHAGE K1F (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.55 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 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 8, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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)449,01921
Polymers444,7926
Non-polymers4,22715
Water16,592921
1
A: ENDO-ALPHA-SIALIDASE
B: ENDO-ALPHA-SIALIDASE
C: ENDO-ALPHA-SIALIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,20910
Polymers222,3963
Non-polymers1,8137
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)224,81011
Polymers222,3963
Non-polymers2,4148
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)99.540, 131.400, 346.040
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-2080-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.498, -0.451, -0.74), (0.46, 0.586, -0.667), (0.735, -0.673, -0.085)108.148, 26.545, 43.726
2given(-0.506, 0.459, 0.73), (-0.446, 0.586, -0.677), (-0.738, -0.668, -0.092)10.262, 62.398, 101.809
3given(-1, 0.006, -0.005), (-0.005, -0.958, -0.287), (-0.006, -0.287, 0.958)24.283, 21.578, 3.713
4given(0.505, -0.453, -0.735), (0.645, -0.367, 0.67), (-0.573, -0.812, 0.107)14.079, -67.688, 82.932
5given(0.498, 0.458, 0.737), (-0.65, -0.366, 0.666), (0.574, -0.81, 0.116)-83.859, -16.785, 37.343

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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: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-alpha-neuraminic acid


Type: oligosaccharide / Mass: 600.525 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-8DNeup5Aca2-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[Aad21122h-2a_2-6_5*NCC/3=O]/1-1/a8-b2WURCSPDB2Glycan 1.1.0
[][a-D-Neup5Ac]{[(8+2)][a-D-Neup5Ac]{}}LINUCSPDB-CARE
#3: Sugar
ChemComp-SLB / N-acetyl-beta-neuraminic acid / N-acetylneuraminic acid / sialic acid / O-sialic acid / 5-N-ACETYL-BETA-D-NEURAMINIC ACID / BETA-SIALIC ACID


Type: D-saccharide, beta linking / Mass: 309.270 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C11H19NO9
IdentifierTypeProgram
DNeup5AcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-neuraminic acidCOMMON NAMEGMML 1.0
b-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 921 / 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: 2.54 Å3/Da / Density % sol: 51.65 %
Crystal growpH: 7.5 / Details: pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9195
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9195 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2.55→2.7 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 2.4 / % possible all: 79.8

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.2315 6565 5 %RANDOM
Rwork0.18005 ---
obs0.18263 124204 88.4 %-
Displacement parametersBiso mean: 21.406 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å20 Å2
2--1.8 Å20 Å2
3----2.3 Å2
Refinement stepCycle: LAST / Resolution: 2.55→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31380 0 279 921 32580

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