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

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Basic information

Entry
Database: PDB / ID: 5fqh
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 / PHOSPHATE ION / Uncharacterized protein
Function and homology information
Biological speciesCLOSTRIDIUM PERFRINGENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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: Atomic model / Data collection ...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_struct_special_symmetry / 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 / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_dist_value / _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_asym_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: 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
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
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)70,8733
Polymers70,2321
Non-polymers6402
Water2,990166
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)111.130, 111.130, 95.770
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-2035-

HOH

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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-(1-4)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 545.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpNAcb1-4DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5][a2112h-1b_1-5][a2112h-1b_1-5_2*NCC/3=O]/1-2-3/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(4+1)][b-D-GalpNAc]{}}}LINUCSPDB-CARE
#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.: 166 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.43 Å3/Da / Density % sol: 49.49 % / 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: 2.1→48.1 Å / Num. obs: 39970 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 10.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.2
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 11 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.9 / % possible all: 99.2

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Processing

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

5fqe


Resolution: 2.1→96.24 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.944 / SU B: 6.024 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.199 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24058 1962 4.9 %RANDOM
Rwork0.18058 ---
obs0.18354 38008 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.214 Å2
Baniso -1Baniso -2Baniso -3
1-0.92 Å20.46 Å20 Å2
2--0.92 Å20 Å2
3----2.98 Å2
Refinement stepCycle: LAST / Resolution: 2.1→96.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4693 0 42 166 4901
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.024862
X-RAY DIFFRACTIONr_bond_other_d0.0010.024390
X-RAY DIFFRACTIONr_angle_refined_deg1.4751.9416612
X-RAY DIFFRACTIONr_angle_other_deg0.759310122
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5685580
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.11424.979241
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.01215800
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2011518
X-RAY DIFFRACTIONr_chiral_restr0.0830.2708
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025530
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021162
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_it2.9424.4882323
X-RAY DIFFRACTIONr_mcbond_other2.9294.4882322
X-RAY DIFFRACTIONr_mcangle_it4.1676.7262902
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.6554.8072537
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: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 120 -
Rwork0.287 2776 -
obs--98.94 %

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