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- PDB-8r73: Polysaccharide lyase BcPL33HA (BcellWH2_04512) Apo form -

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Basic information

Entry
Database: PDB / ID: 8r73
TitlePolysaccharide lyase BcPL33HA (BcellWH2_04512) Apo form
ComponentsHeparinase II/III-like protein
KeywordsLYASE / Polysaccharide lyase / glycosaminoglycan / Hyaluronic acid / conformational change
Function / homologyHeparinase II/III-like / Heparinase II/III-like, C-terminal / Chondroitin AC/alginate lyase / lyase activity / Heparinase II/III-like protein
Function and homology information
Biological speciesBacteroides cellulosilyticus WH2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsCartmell, A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Royal Society212050 United Kingdom
Wellcome Trust1065163470 United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: Bacterial polysaccharide lyase family 33: Specificity from an evolutionarily conserved binding tunnel.
Authors: Loiodice, M. / Drula, E. / McIver, Z. / Antonyuk, S. / Basle, A. / Lima, M. / Yates, E.A. / Byrne, D.P. / Coughlan, J. / Leech, A. / Mesdaghi, S. / Rigden, D.J. / Drouillard, S. / Helbert, W. ...Authors: Loiodice, M. / Drula, E. / McIver, Z. / Antonyuk, S. / Basle, A. / Lima, M. / Yates, E.A. / Byrne, D.P. / Coughlan, J. / Leech, A. / Mesdaghi, S. / Rigden, D.J. / Drouillard, S. / Helbert, W. / Henrissat, B. / Terrapon, N. / Wright, G.S.A. / Couturier, M. / Cartmell, A.
History
DepositionNov 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2025Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Feb 26, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Mar 5, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heparinase II/III-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8432
Polymers72,7781
Non-polymers651
Water5,621312
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.63, 91.39, 84.77
Angle α, β, γ (deg.)90, 109.28, 90
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-917-

HOH

21A-1093-

HOH

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Components

#1: Protein Heparinase II/III-like protein


Mass: 72777.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides cellulosilyticus WH2 (bacteria)
Gene: BcellWH2_04512 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0P0GKX0
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.6 Å3/Da / Density % sol: 52.75 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10 % PEG 8000 8 % Ethylene glycol 0.1 M HEPES pH 7.5 28 mg/ml

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 23, 2023
RadiationMonochromator: 0.96 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.11→40.01 Å / Num. obs: 42837 / % possible obs: 99.7 % / Redundancy: 6.7 % / CC1/2: 1 / Net I/σ(I): 10.8
Reflection shellResolution: 2.11→2.17 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3507 / CC1/2: 0.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.11→40.008 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.928 / SU B: 6.432 / SU ML: 0.161 / Cross valid method: FREE R-VALUE / ESU R: 0.211 / ESU R Free: 0.194
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2502 2098 4.898 %
Rwork0.1888 40738 -
all0.192 --
obs-42836 99.721 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 42.933 Å2
Baniso -1Baniso -2Baniso -3
1-0.029 Å2-0 Å20.781 Å2
2--1.831 Å20 Å2
3----1.933 Å2
Refinement stepCycle: LAST / Resolution: 2.11→40.008 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4981 0 1 312 5294
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0125109
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164709
X-RAY DIFFRACTIONr_angle_refined_deg1.8261.8176929
X-RAY DIFFRACTIONr_angle_other_deg0.6131.76510816
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1555616
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.723532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.86910859
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.93410253
X-RAY DIFFRACTIONr_chiral_restr0.090.2726
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026170
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021278
X-RAY DIFFRACTIONr_nbd_refined0.2150.21042
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.24329
X-RAY DIFFRACTIONr_nbtor_refined0.1880.22486
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.22729
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2283
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1530.25
X-RAY DIFFRACTIONr_nbd_other0.1380.269
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.160.228
X-RAY DIFFRACTIONr_mcbond_it3.7744.0452467
X-RAY DIFFRACTIONr_mcbond_other3.7714.0452467
X-RAY DIFFRACTIONr_mcangle_it4.8127.2723082
X-RAY DIFFRACTIONr_mcangle_other4.8137.2733083
X-RAY DIFFRACTIONr_scbond_it4.7914.4262642
X-RAY DIFFRACTIONr_scbond_other4.794.4272643
X-RAY DIFFRACTIONr_scangle_it6.7217.9423847
X-RAY DIFFRACTIONr_scangle_other6.7217.9433848
X-RAY DIFFRACTIONr_lrange_it7.95539.8315953
X-RAY DIFFRACTIONr_lrange_other7.96639.4155898
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.11-2.1650.3271560.30629960.30731530.9230.92999.96830.287
2.165-2.2240.3241480.27629200.27930690.9310.94699.96740.251
2.224-2.2880.3551350.25928370.26329790.9280.95499.7650.231
2.288-2.3580.2961430.23127670.23429100.9420.9631000.198
2.358-2.4350.3171510.22926560.23428080.9370.96699.96440.195
2.435-2.520.2851300.21925900.22227210.9440.97199.96320.186
2.52-2.6150.2761140.18725210.1926400.9520.97999.81060.158
2.615-2.7220.2581230.18424080.18825390.9610.9899.68490.158
2.722-2.8420.2651140.19523080.19924380.9550.97799.34370.17
2.842-2.980.2361140.17422080.17723340.9650.98299.48590.158
2.98-3.140.2631050.19121330.19422490.9570.98199.51090.179
3.14-3.3290.2761110.21319530.21620720.9470.97699.61390.203
3.329-3.5570.247910.21118750.21219690.9680.97999.84760.205
3.557-3.840.218810.17917700.18118530.9740.98499.89210.179
3.84-4.2030.198760.14516010.14816780.9760.98899.94040.151
4.203-4.6920.21890.13614530.1415500.980.9999.48390.15
4.692-5.4060.218810.1512690.15413750.9760.98998.18180.167
5.406-6.5910.293620.18810860.19411510.9520.98399.73940.203
6.591-9.1970.186470.1778710.1789180.980.9831000.205
9.197-40.0080.251270.1675160.1715430.9650.9851000.2

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