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- PDB-6pwi: Structure of CpGH84D -

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Basic information

Entry
Database: PDB / ID: 6pwi
TitleStructure of CpGH84D
ComponentsPutative hyaluronoglucosaminidase
KeywordsHYDROLASE / Glycoside Hydrolase
Function / homology
Function and homology information


carbohydrate derivative metabolic process / beta-N-acetylglucosaminidase activity / carbohydrate metabolic process / membrane
Similarity search - Function
FIVAR domain / Beta-N-acetylglucosaminidase / beta-N-acetylglucosaminidase / Glycosyl hydrolases family 84 (GH84) domain profile. / : / 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 ...FIVAR domain / Beta-N-acetylglucosaminidase / beta-N-acetylglucosaminidase / Glycosyl hydrolases family 84 (GH84) domain profile. / : / 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 / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Putative hyaluronoglucosaminidase
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.65 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 23, 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 hyaluronoglucosaminidase
B: Putative hyaluronoglucosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,12315
Polymers143,3162
Non-polymers80713
Water9,206511
1
A: Putative hyaluronoglucosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0928
Polymers71,6581
Non-polymers4347
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative hyaluronoglucosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0307
Polymers71,6581
Non-polymers3726
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)195.723, 195.723, 106.467
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Putative hyaluronoglucosaminidase


Mass: 71657.938 Da / Num. of mol.: 2
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_1487 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H2YV83
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 511 / 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: 4.11 Å3/Da / Density % sol: 70.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 25% PEG4000, 0.2 M (NH4)2SO4 and 0.1 M sodium citrate:HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9791 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: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.65→38.92 Å / Num. obs: 66655 / % possible obs: 98.8 % / Redundancy: 5.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.062 / Net I/σ(I): 14.3
Reflection shellResolution: 2.65→2.71 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.477 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 4477 / CC1/2: 0.778 / Rpim(I) all: 0.324 / % possible all: 99.3

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Phasing

PhasingMethod: molecular replacement

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Processing

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

2v5c


Resolution: 2.65→38.92 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.918 / SU B: 8.153 / SU ML: 0.163 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.308 / ESU R Free: 0.225 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2083 3369 5.1 %RANDOM
Rwork0.171 ---
obs0.1729 63286 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 113.25 Å2 / Biso mean: 36.715 Å2 / Biso min: 10.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å2-0.1 Å20 Å2
2---0.2 Å20 Å2
3---0.64 Å2
Refinement stepCycle: final / Resolution: 2.65→38.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9526 0 52 512 10090
Biso mean--49.03 31.41 -
Num. residues----1193
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0129806
X-RAY DIFFRACTIONr_angle_refined_deg1.0361.63313264
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.18651193
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.85224.343525
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.831151658
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8161534
X-RAY DIFFRACTIONr_chiral_restr0.0920.21254
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027562
LS refinement shellResolution: 2.65→2.719 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 210 -
Rwork0.243 4711 -
all-4921 -
obs--99.35 %

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