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- PDB-3gvj: Crystal structure of an endo-neuraminidaseNF mutant -

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Basic information

Entry
Database: PDB / ID: 3gvj
TitleCrystal structure of an endo-neuraminidaseNF mutant
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 / 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
Tail spike protein / Tail spike protein
Similarity search - Component
Biological speciesEnterobacteria phage K1F (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.48 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: Advisory / 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_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_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.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 13, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)77,1143
Polymers74,4561
Non-polymers2,6572
Water15,313850
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)231,3419
Polymers223,3693
Non-polymers7,9726
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 area51920 Å2
ΔGint-145 kcal/mol
Surface area67290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.090, 119.090, 175.980
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-1096-

HOH

21A-1420-

HOH

31A-1485-

HOH

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Components

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


Mass: 74456.336 Da / Num. of mol.: 1 / Fragment: residues 246-910 / Mutation: R647A
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-alpha-neuraminic acid-(2-8)-N-acetyl-alpha-neuraminic ...N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-beta-neuraminic acid


Type: oligosaccharide / Mass: 1474.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-8DNeup5Aca2-8DNeup5Aca2-8DNeup5Aca2-8DNeup5Acb2-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[Aad21122h-2b_2-6_5*NCC/3=O][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-2-2-2/a8-b2_b8-c2_c8-d2_d8-e2WURCSPDB2Glycan 1.1.0
[][b-D-Neup5Ac]{[(8+2)][a-D-Neup5Ac]{[(8+2)][a-D-Neup5Ac]{[(8+2)][a-D-Neup5Ac]{[(8+2)][a-D-Neup5Ac]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-alpha-neuraminic ...N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-beta-neuraminic acid


Type: oligosaccharide / Mass: 1183.034 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-8DNeup5Aca2-8DNeup5Aca2-8DNeup5Acb2-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[Aad21122h-2b_2-6_5*NCC/3=O][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-2-2/a8-b2_b8-c2_c8-d2WURCSPDB2Glycan 1.1.0
[][b-D-Neup5Ac]{[(8+2)][a-D-Neup5Ac]{[(8+2)][a-D-Neup5Ac]{[(8+2)][a-D-Neup5Ac]{}}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 850 / 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: 3.23 Å3/Da / Density % sol: 61.87 %
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: 1.4→20 Å / Num. obs: 164778 / % possible obs: 89.9 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.09
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.4-1.50.3594146.2
1.5-1.60.3164.7199.8
1.6-1.650.2735.71100
1.65-1.70.2546199.9
1.7-1.750.2316.81100
1.75-1.850.2057.31100
1.85-20.1628.81100
2-2.20.12610.61100
2.2-2.30.10612.31100
2.3-2.50.112.81100
2.5-2.80.08714.71100
2.8-30.08161100
3-40.06719.61100
4-50.05423.41100
5-60.0526.81100
6-100.04627.61100
10-200.04528199.8
201

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMAC5.5.0039refinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→12 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 0.1 / SU B: 1.524 / SU ML: 0.05 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21636 7739 5 %RANDOM
Rwork0.19395 ---
obs0.19506 147036 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: 16.438 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20.12 Å20 Å2
2--0.24 Å20 Å2
3----0.37 Å2
Refinement stepCycle: LAST / Resolution: 1.48→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5253 0 182 850 6285
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0215787
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4711.9677925
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0955723
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.34623.488281
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.88715853
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9121543
X-RAY DIFFRACTIONr_chiral_restr0.1310.2866
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214567
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_it0.5151.53431
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.8825587
X-RAY DIFFRACTIONr_scbond_it1.50532356
X-RAY DIFFRACTIONr_scangle_it2.2284.52319
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.48→1.518 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 564 -
Rwork0.278 10697 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.7031-0.2032-0.17061.0908-0.02380.60630.0049-0.21460.0920.03810.0018-0.07640.00760.0233-0.00670.00380.0001-0.00090.0287-0.00930.009650.32247.563233.1273
20.1403-0.03080.02420.1475-0.04830.4466-0.00460.01870.0171-0.0225-0.0019-0.0132-0.00780.00460.00640.0045-0.00110.0010.00250.00210.002761.559735.809-44.5517
30.80520.120.50340.55530.10690.45790.07320.0084-0.11080.028-0.0023-0.030.0405-0.0319-0.07090.02410.0007-0.03350.00990.00130.047334.40633.479-12.391
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A245 - 275
2X-RAY DIFFRACTION2A777 - 910
3X-RAY DIFFRACTION3A423 - 511

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