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- PDB-3gvl: Crystal Structure of endo-neuraminidaseNF -

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Basic information

Entry
Database: PDB / ID: 3gvl
TitleCrystal Structure of endo-neuraminidaseNF
ComponentsEndo-N-acetylneuraminidase
KeywordsHYDROLASE / endo-neuraminidase / polysialic acid / triple-beta helix / 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
Endosialidase, N-terminal extension domain / Endosialidase, domain 4 / Endosialidase, domain 4 / Glycosyl hydrolase 58 / Endosialidase, beta barrel domain / 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 ...Endosialidase, N-terminal extension domain / Endosialidase, domain 4 / Endosialidase, domain 4 / Glycosyl hydrolase 58 / Endosialidase, beta barrel domain / 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 / Endosialidase, C-terminal domain superfamily / Intramolecular chaperone auto-processing domain / Tail spike TSP1/Gp66, N-terminal domain / Chaperone of endosialidase / Tail spike TSP1/Gp66 receptor binding N-terminal 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
N-acetyl-beta-neuraminic acid / Tail spike protein / Tail spike protein
Similarity search - Component
Biological speciesEnterobacteria phage K1F (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.41 Å
AuthorsSchulz, E.C. / Dickmanns, A. / Ficner, R.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structural basis for the recognition and cleavage of polysialic acid by the bacteriophage K1F tailspike protein EndoNF.
Authors: Schulz, E.C. / Schwarzer, D. / Frank, M. / Stummeyer, K. / Muhlenhoff, M. / Dickmanns, A. / Gerardy-Schahn, R. / Ficner, R.
History
DepositionMar 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site.occupancy / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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 2.1Feb 21, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endo-N-acetylneuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,4523
Polymers74,5421
Non-polymers9102
Water25,2391401
1
A: Endo-N-acetylneuraminidase
hetero molecules

A: Endo-N-acetylneuraminidase
hetero molecules

A: Endo-N-acetylneuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,3579
Polymers223,6273
Non-polymers2,7296
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area45750 Å2
ΔGint-189 kcal/mol
Surface area66240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.092, 119.092, 175.981
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-978-

HOH

21A-1370-

HOH

31A-1775-

HOH

41A-1915-

HOH

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Components

#1: Protein Endo-N-acetylneuraminidase / Endo-alpha-sialidase / Gp17 protein


Mass: 74542.461 Da / Num. of mol.: 1 / Fragment: residues 246-910
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage K1F (virus) / Gene: sia, 17, 17.0 / 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-beta-neuraminic acid


Type: oligosaccharide / Mass: 600.525 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-8DNeup5Acb2-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[Aad21122h-2b_2-6_5*NCC/3=O][Aad21122h-2a_2-6_5*NCC/3=O]/1-2/a8-b2WURCSPDB2Glycan 1.1.0
[][b-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.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1401 / 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: 3.22 Å3/Da / Density % sol: 61.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 20% (w/v) PEG 8000, 0.1M Tris/HCl, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.41→19.64 Å / Num. obs: 184838 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.074
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.41-1.450.532.41100
1.45-1.490.43631100
1.49-1.530.363.81100
1.53-1.580.3064.51100
1.58-1.630.2595.41100
1.63-1.690.2266.21100
1.69-1.750.1897.6199.9
1.75-1.820.1569.3199.8
1.82-1.90.13210.9199.5
1.9-1.990.10613.6199.3
1.99-2.10.08716.5199
2.1-2.230.07518.8198.9
2.23-2.380.06620.7199.2
2.38-2.570.05722199.8
2.57-2.820.04724.81100
2.82-3.150.0428.21100
3.15-3.640.03533.81100
3.64-4.460.03237.31100
4.46-6.310.02837.7199.8
6.310.02538.1195.8

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.5.0039refinement
PDB_EXTRACT3.006data extraction
RefinementResolution: 1.41→19.64 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / Occupancy max: 1 / Occupancy min: 0 / SU B: 0.985 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18769 8949 5 %RANDOM
Rwork0.1685 ---
obs0.16946 170020 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.008 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å2-0.03 Å20 Å2
2---0.07 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.41→19.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5259 0 62 1401 6722
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0225763
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4341.9467937
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0715768
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.2823.803284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.46715890
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.21539
X-RAY DIFFRACTIONr_chiral_restr0.140.2862
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214587
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.471.53483
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.87625707
X-RAY DIFFRACTIONr_scbond_it1.41932280
X-RAY DIFFRACTIONr_scangle_it2.1444.52180
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.41→1.446 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 662 -
Rwork0.248 12566 -
obs--100 %

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