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- PDB-5fr0: The details of glycolipid glycan hydrolysis by the structural ana... -

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Basic information

Entry
Database: PDB / ID: 5fr0
TitleThe details of glycolipid glycan hydrolysis by the structural analysis of a family 123 glycoside hydrolase from Clostridium perfringens
ComponentsBETA-N-ACETYLGALACTOSAMINIDASE
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE / GH123 / GLYCOSPHINGOLIPID / GANGLIOSIDE / GLOBOSIDE / SUBSTRATE-ASSISTED CATALYSIS.
Function / homologyGlycoside hydrolase 123, N-terminal domain / Glycoside hydrolase 123, N-terminal domain / Glycoside hydrolase 123, C-terminal / Glycoside hydrolase 123, catalytic domain / PHOSPHATE ION / Chem-SIZ / Uncharacterized protein
Function and homology information
Biological speciesCLOSTRIDIUM PERFRINGENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsNoach, I. / Pluvinage, B. / Laurie, C. / Abe, K.T. / Alteen, M. / Vocadlo, D.J. / Boraston, A.B.
CitationJournal: J.Mol.Biol. / Year: 2016
Title: The Details of Glycolipid Glycan Hydrolysis by the Structural Analysis of a Family 123 Glycoside Hydrolase from Clostridium Perfringens
Authors: Noach, I. / Pluvinage, B. / Laurie, C. / Abe, K.T. / Alteen, M. / Vocadlo, D.J. / Boraston, A.B.
History
DepositionDec 14, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2016Group: Database references
Revision 1.2Aug 24, 2016Group: Database references
Revision 1.3Jul 29, 2020Group: Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jan 10, 2024Group: 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

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Assembly

Deposited unit
A: BETA-N-ACETYLGALACTOSAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5863
Polymers70,2341
Non-polymers3522
Water7,476415
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.530, 99.530, 95.310
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein BETA-N-ACETYLGALACTOSAMINIDASE


Mass: 70234.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM PERFRINGENS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: A0A0H2YNR7
#2: Sugar ChemComp-SIZ / 2-deoxy-2-[(difluoroacetyl)amino]-beta-D-galactopyranose / N-DIFLUOROACETYL-D-GALACTOSAMINE / N-difluoroacetyl-beta-D-galactosamine / 2-deoxy-2-[(difluoroacetyl)amino]-beta-D-galactose / 2-deoxy-2-[(difluoroacetyl)amino]-D-galactose / 2-deoxy-2-[(difluoroacetyl)amino]-galactose


Type: D-saccharide, beta linking / Mass: 257.189 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H13F2NO6
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / 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: 1.94 Å3/Da / Density % sol: 36.72 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.984
DetectorDetector: CCD / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 1.75→47.7 Å / Num. obs: 55369 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 12.6 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.7
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5FQE

5fqe


Resolution: 1.75→95.31 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.202 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22099 2713 4.9 %RANDOM
Rwork0.18074 ---
obs0.18274 52619 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.234 Å2
Baniso -1Baniso -2Baniso -3
1-1.03 Å20.51 Å20 Å2
2--1.03 Å20 Å2
3----3.33 Å2
Refinement stepCycle: LAST / Resolution: 1.75→95.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4623 0 22 415 5060
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.024797
X-RAY DIFFRACTIONr_bond_other_d0.0020.024327
X-RAY DIFFRACTIONr_angle_refined_deg1.641.9366528
X-RAY DIFFRACTIONr_angle_other_deg0.8693.0029979
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7795582
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.9425.127236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.88215788
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8981517
X-RAY DIFFRACTIONr_chiral_restr0.10.2699
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215501
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021140
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_it2.7783.412322
X-RAY DIFFRACTIONr_mcbond_other2.7783.4082321
X-RAY DIFFRACTIONr_mcangle_it3.6925.1042906
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.2483.6642474
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 180 -
Rwork0.253 3867 -
obs--99.88 %

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