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- PDB-3ju4: Crystal Structure Analysis of EndosialidaseNF at 0.98 A Resolution -

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Basic information

Entry
Database: PDB / ID: 3ju4
TitleCrystal Structure Analysis of EndosialidaseNF at 0.98 A Resolution
ComponentsEndo-N-acetylneuraminidase
KeywordsHYDROLASE / 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 / 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
N-acetyl-beta-neuraminic acid / Tail spike protein
Similarity search - Component
Biological speciesEnterobacteria phage K1F (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.98 Å
AuthorsSchulz, E.C. / Neuman, P. / Gerardy-Schahn, R. / Sheldrick, G.M. / Ficner, R.
CitationJournal: 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
DepositionSep 14, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 18, 2012Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.ptnr1_label_seq_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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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)75,0528
Polymers74,5421
Non-polymers5107
Water29,1121616
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)225,15624
Polymers223,6273
Non-polymers1,52921
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 area44390 Å2
ΔGint-271 kcal/mol
Surface area65530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.040, 119.040, 175.690
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-1087-

HOH

21A-1088-

HOH

31A-2256-

HOH

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Components

#1: Protein Endo-N-acetylneuraminidase / endoNF / Endo-N / Endosialidase / G102


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
#2: 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
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1616 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE DEPOSITORS STATE THAT RESIDUE 628 IS HIS AND THAT UNIPROT IS INCORRECT AT THIS POSITION.

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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: 3.21 Å3/Da / Density % sol: 61.73 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 20, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameClassification
DNAdata collection
MOLREPphasing
SHELXL-97refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1V0E

1v0e


Resolution: 0.98→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1334 25843 -RANDOM
Rwork0.1162 ---
obs0.1162 516832 96.9 %-
Refine analyzeNum. disordered residues: 43
Refinement stepCycle: LAST / Resolution: 0.98→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5260 0 27 1616 6903

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