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- PDB-6pv5: Structure of CpGH84B -

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Basic information

Entry
Database: PDB / ID: 6pv5
TitleStructure of CpGH84B
ComponentsPutative O-GlcNAcase nagJ
KeywordsHYDROLASE / Glycoside Hydrolase
Function / homology
Function and homology information


carbohydrate derivative metabolic process / beta-N-acetylglucosaminidase activity / carbohydrate metabolic process
Similarity search - Function
: / Hyaluronidase post-catalytic domain-like / Beta-N-acetylglucosaminidase / beta-N-acetylglucosaminidase / Glycosyl hydrolases family 84 (GH84) domain profile. / : / Chitobiase/beta-hexosaminidase domain 2-like / Chitobiase; domain 2 / Beta-hexosaminidase, bacterial type, N-terminal / Glycosyl hydrolase family 20, domain 2 ...: / Hyaluronidase post-catalytic domain-like / Beta-N-acetylglucosaminidase / beta-N-acetylglucosaminidase / Glycosyl hydrolases family 84 (GH84) domain profile. / : / Chitobiase/beta-hexosaminidase domain 2-like / Chitobiase; domain 2 / Beta-hexosaminidase, bacterial type, N-terminal / Glycosyl hydrolase family 20, domain 2 / Beta-hexosaminidase-like, domain 2 / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Galactose-binding-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative O-GlcNAcase nagJ
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.18 Å
AuthorsPluvinage, B. / Boraston, A.B.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Glycobiology / Year: 2019
Title: Structural and functional analysis of four family 84 glycoside hydrolases from the opportunistic pathogen Clostridium perfringens.
Authors: Pluvinage, B. / Massel, P.M. / Burak, K. / Boraston, A.B.
History
DepositionJul 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jan 1, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Putative O-GlcNAcase nagJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1936
Polymers70,8821
Non-polymers3105
Water4,197233
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint13 kcal/mol
Surface area23340 Å2
Unit cell
Length a, b, c (Å)171.389, 171.389, 128.797
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-743-

HOH

21A-774-

HOH

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Components

#1: Protein Putative O-GlcNAcase nagJ


Mass: 70882.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (strain ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A) (bacteria)
Strain: ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A
Gene: CPF_0875 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H2YTZ1
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.57 Å3/Da / Density % sol: 52.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris HCl and 2.0 M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.18→39.24 Å / Num. obs: 37842 / % possible obs: 100 % / Redundancy: 9.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.027 / Net I/σ(I): 18.2
Reflection shellResolution: 2.18→2.3 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 5.8 / Num. unique obs: 5487 / CC1/2: 0.943 / Rpim(I) all: 0.168 / % possible all: 99.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0253refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V5C

2v5c


Resolution: 2.18→39.24 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.93 / SU B: 5.221 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.216 / ESU R Free: 0.189 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2368 1861 4.9 %RANDOM
Rwork0.1884 ---
obs0.1908 35974 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 115.62 Å2 / Biso mean: 43.243 Å2 / Biso min: 15.33 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20.27 Å20 Å2
2--0.54 Å20 Å2
3----1.74 Å2
Refinement stepCycle: final / Resolution: 2.18→39.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4339 0 20 234 4593
Biso mean--50.64 45.62 -
Num. residues----567
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0124492
X-RAY DIFFRACTIONr_angle_refined_deg1.2961.6326095
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6795574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.35624.318220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.34815718
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.981516
X-RAY DIFFRACTIONr_chiral_restr0.0940.2600
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023460
LS refinement shellResolution: 2.18→2.237 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 150 -
Rwork0.254 2597 -
all-2747 -
obs--99.46 %

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