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- PDB-2vo8: Cohesin module from Clostridium perfringens ATCC13124 family 33 g... -

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Basic information

Entry
Database: PDB / ID: 2vo8
TitleCohesin module from Clostridium perfringens ATCC13124 family 33 glycoside hydrolase.
ComponentsEXO-ALPHA-SIALIDASE
KeywordsHYDROLASE / COHESIN / HIGH AFFINITY / GLYCOSIDE HYDROLASE / CLOSTRIDIUM PERFRINGENS
Function / homology
Function and homology information


exo-alpha-sialidase activity / exo-alpha-sialidase / carbohydrate binding / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Immunoglobulin-like - #680 / Glycoside hydrolase, family 33, N-terminal / Trans-sialidase, domain 3 / Sialidase, N-terminal domain / BNR repeat-like domain / Sialidase family / Sialidase / CBM2/CBM3, carbohydrate-binding domain superfamily / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain ...Immunoglobulin-like - #680 / Glycoside hydrolase, family 33, N-terminal / Trans-sialidase, domain 3 / Sialidase, N-terminal domain / BNR repeat-like domain / Sialidase family / Sialidase / CBM2/CBM3, carbohydrate-binding domain superfamily / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Sialidase superfamily / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Galactose-binding-like domain superfamily / Fibronectin type III / Fibronectin type III superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
exo-alpha-sialidase / Sialidase
Similarity search - Component
Biological speciesCLOSTRIDIUM PERFRINGENS (bacteria)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 1.7 Å
AuthorsGregg, K. / Adams, J.J. / Bayer, E.A. / Boraston, A.B. / Smith, S.P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Structural Basis of Clostridium Perfringens Toxin Complex Formation.
Authors: Adams, J.J. / Gregg, K. / Bayer, E.A. / Boraston, A.B. / Smith, S.P.
History
DepositionFeb 8, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
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

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Assembly

Deposited unit
A: EXO-ALPHA-SIALIDASE


Theoretical massNumber of molelcules
Total (without water)15,3771
Polymers15,3771
Non-polymers00
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)38.088, 38.088, 174.851
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein EXO-ALPHA-SIALIDASE / FAMILY 33 GLYCOSIDE HYDROLASE


Mass: 15377.043 Da / Num. of mol.: 1 / Fragment: COHESIN, RESIDUES 939-1081
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM PERFRINGENS (bacteria) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q0TTQ4, UniProt: A0A0H2YT71*PLUS, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 1.89 Å3/Da / Density % sol: 40.33 % / Description: NONE

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS-IV / Detector: IMAGE PLATE / Details: OSMIC BLUE
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→43.73 Å / Num. obs: 13479 / % possible obs: 93.8 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalCleardata reduction
d*TREKdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.7→43.73 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.073 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.258 713 5 %RANDOM
Rwork0.214 ---
obs0.217 13479 93.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20 Å2
2--0.21 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.7→43.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1024 0 0 164 1188
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221045
X-RAY DIFFRACTIONr_bond_other_d0.0010.02667
X-RAY DIFFRACTIONr_angle_refined_deg1.8811.9841419
X-RAY DIFFRACTIONr_angle_other_deg0.97831666
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5735138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.01227.6647
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.08415189
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.52151
X-RAY DIFFRACTIONr_chiral_restr0.1150.2173
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021176
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02177
X-RAY DIFFRACTIONr_nbd_refined0.1960.2150
X-RAY DIFFRACTIONr_nbd_other0.1910.2669
X-RAY DIFFRACTIONr_nbtor_refined0.1650.2491
X-RAY DIFFRACTIONr_nbtor_other0.0910.2591
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2070.2112
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3640.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1470.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3861.5889
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.56721088
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7623443
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4164.5329
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.313 55
Rwork0.309 888

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