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- PDB-1kit: VIBRIO CHOLERAE NEURAMINIDASE -

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Basic information

Entry
Database: PDB / ID: 1kit
TitleVIBRIO CHOLERAE NEURAMINIDASE
ComponentsSIALIDASE
KeywordsHYDROLASE / GLYCOSIDASE / CALCIUM
Function / homology
Function and homology information


: / : / : / metabolic process / sialic acid binding / ganglioside catabolic process / oligosaccharide catabolic process / exo-alpha-sialidase / exo-alpha-sialidase activity / intracellular membrane-bounded organelle ...: / : / : / metabolic process / sialic acid binding / ganglioside catabolic process / oligosaccharide catabolic process / exo-alpha-sialidase / exo-alpha-sialidase activity / intracellular membrane-bounded organelle / extracellular region / membrane / cytoplasm
Similarity search - Function
Vibrio cholerae neuraminidase, lectin-like domain / Vibrio cholerae sialidase, lectin insertion / BNR repeat-like domain / Sialidase family / Sialidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Jelly Rolls - #200 ...Vibrio cholerae neuraminidase, lectin-like domain / Vibrio cholerae sialidase, lectin insertion / BNR repeat-like domain / Sialidase family / Sialidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Sialidase / Sialidase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsTaylor, G.L. / Crennell, S.J. / Garman, E.F. / Vimr, E.R. / Laver, W.G.
Citation
Journal: Structure / Year: 1994
Title: Crystal structure of Vibrio cholerae neuraminidase reveals dual lectin-like domains in addition to the catalytic domain.
Authors: Crennell, S. / Garman, E. / Laver, G. / Vimr, E. / Taylor, G.
#1: Journal: J.Mol.Biol. / Year: 1992
Title: Purification, Crystallization and Preliminary Crystallographic Study of Neuraminidase from Vibrio Cholerae and Salmonella Typhimurium Lt2
Authors: Taylor, G. / Vimr, E. / Garman, E. / Laver, G.
History
DepositionJun 21, 1996Processing site: BNL
Revision 1.0Jun 5, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SIALIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,1203
Polymers83,0391
Non-polymers802
Water12,592699
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.300, 78.900, 164.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SIALIDASE / NEURAMINIDASE


Mass: 83039.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: CLASSICAL OGAWA 395 / Gene: NANH / Plasmid: PCVD364 / Gene (production host): NANH / Production host: Escherichia coli (E. coli)
References: UniProt: P37060, UniProt: P0C6E9*PLUS, exo-alpha-sialidase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 699 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 %PEG33501reservoir
25 mM1reservoirCaCl2

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 40491 / % possible obs: 95 % / Observed criterion σ(I): 1 / Redundancy: 9.15 % / Rmerge(I) obs: 0.098
Reflection
*PLUS
Highest resolution: 2.3 Å / Num. measured all: 370535

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Processing

Software
NameVersionClassification
TNT5Crefinement
DENZOdata reduction
RefinementResolution: 2.3→20 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.17 --
obs-40555 95 %
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5859 0 2 699 6560
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_bond_d0.014
X-RAY DIFFRACTIONt_angle_deg1.392
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes0.0125
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Version: 5C / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.17 / Rfactor Rwork: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_plane_restr / Dev ideal: 0.012 / Weight: 5

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