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

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Basic information

Entry
Database: PDB / ID: 5fqg
TitleThe details of glycolipid glycan hydrolysis by the structural analysis of a family 123 glycoside hydrolase from Clostridium perfringens
ComponentsBETA-N-ACETYLGALACTOSAMINIDASE
KeywordsHYDROLASE / BETA-N-ACETYLGALACTOSAMINIDASE / 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 / FORMIC ACID / Uncharacterized protein
Function and homology information
Biological speciesCLOSTRIDIUM PERFRINGENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 10, 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 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_unobs_or_zero_occ_atoms / 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 / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _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_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 2.1Jan 10, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AD" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AD" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA-N-ACETYLGALACTOSAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8006
Polymers70,2321
Non-polymers5675
Water3,495194
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)113.340, 113.340, 95.951
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: 70232.266 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM PERFRINGENS (bacteria) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: A0A0H2YNR7
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpNAcb1-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][a2112h-1b_1-5_2*NCC/3=O]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+1)][b-D-GalpNAc]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.66 Å3/Da / Density % sol: 53.71 % / 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: 2.3→68 Å / Num. obs: 32038 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 15.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 16.7
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 15 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 4.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FQE

5fqe


Resolution: 2.3→98.16 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.921 / SU B: 9.978 / SU ML: 0.229 / Cross valid method: THROUGHOUT / ESU R: 0.358 / ESU R Free: 0.257 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27279 1495 4.7 %RANDOM
Rwork0.22592 ---
obs0.22808 30513 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: 46.979 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.3→98.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4714 0 38 194 4946
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.024872
X-RAY DIFFRACTIONr_bond_other_d0.0020.024386
X-RAY DIFFRACTIONr_angle_refined_deg1.2821.9376622
X-RAY DIFFRACTIONr_angle_other_deg0.906310111
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.75584
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.15625.021243
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.72615796
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7411518
X-RAY DIFFRACTIONr_chiral_restr0.0740.2709
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025574
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021170
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_it2.2634.7382336
X-RAY DIFFRACTIONr_mcbond_other2.2634.7382337
X-RAY DIFFRACTIONr_mcangle_it3.5977.1022920
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0914.862535
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: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 135 -
Rwork0.357 2203 -
obs--100 %

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