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- PDB-8r71: Polysaccharide lyase BtPL33HA (BT4410) Y291A with HAdp4 collected... -

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Basic information

Entry
Database: PDB / ID: 8r71
TitlePolysaccharide lyase BtPL33HA (BT4410) Y291A with HAdp4 collected at 1.22 A
ComponentsHeparinase
KeywordsLYASE / Polysaccharide lyase / glycosaminoglycan / Hyaluronic acid / conformational change
Function / homologyHeparinase II/III-like / Heparinase II/III-like, C-terminal / Chondroitin AC/alginate lyase / cell envelope / lyase activity / metal ion binding / polyethylene glycol / Heparinase II/III-like C-terminal domain-containing protein
Function and homology information
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 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 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 1.2Mar 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
B: Heparinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,7948
Polymers147,1372
Non-polymers2,6576
Water11,494638
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-65 kcal/mol
Surface area46650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.633, 137.347, 202.832
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ILE / End label comp-ID: ILE / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 19 - 635 / Label seq-ID: 27 - 643

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Heparinase


Mass: 73568.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_4410 / Production host: Escherichia coli (E. coli) / References: UniProt: Q89ZG7
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 600.525 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpAb1-3DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2122A-1b_1-5]/1-2-1/a3-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][b-D-GlcpA]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-P4K / polyethylene glycol / 3,6,9,12,15,18,21,24,27,30,33,36,39,42-tetradecaoxatetratetracontan-1-ol


Mass: 662.804 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H62O15
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 638 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.54 Å3/Da / Density % sol: 51.49 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 20 % PEG 6000 0.1 M MES pH 6.0 0.1 M Ammonium chloride 20 mg/ml

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.22 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.22 Å / Relative weight: 1
ReflectionResolution: 1.92→60.66 Å / Num. obs: 115460 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.999 / Net I/σ(I): 19.9
Reflection shellResolution: 1.92→1.95 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 5594 / CC1/2: 0.824

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→60.66 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / SU B: 6.511 / SU ML: 0.095 / Cross valid method: FREE R-VALUE / ESU R: 0.139 / ESU R Free: 0.127
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2083 5759 4.992 %
Rwork0.179 109599 -
all0.18 --
obs-115358 99.99 %
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: 34.777 Å2
Baniso -1Baniso -2Baniso -3
1-0.428 Å2-0 Å20 Å2
2---0.163 Å20 Å2
3----0.265 Å2
Refinement stepCycle: LAST / Resolution: 1.92→60.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9817 0 105 638 10560
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01210245
X-RAY DIFFRACTIONr_bond_other_d0.0010.0169531
X-RAY DIFFRACTIONr_angle_refined_deg1.7251.83213881
X-RAY DIFFRACTIONr_angle_other_deg0.5971.77921959
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.48251236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.59556
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.29101768
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.48510492
X-RAY DIFFRACTIONr_chiral_restr0.0890.21471
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212195
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022461
X-RAY DIFFRACTIONr_nbd_refined0.2250.22028
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.28813
X-RAY DIFFRACTIONr_nbtor_refined0.1820.25007
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.25375
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2550
X-RAY DIFFRACTIONr_metal_ion_refined0.160.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1420.213
X-RAY DIFFRACTIONr_nbd_other0.2150.267
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2110.213
X-RAY DIFFRACTIONr_mcbond_it2.1172.2814926
X-RAY DIFFRACTIONr_mcbond_other2.1172.2814926
X-RAY DIFFRACTIONr_mcangle_it2.9054.0886168
X-RAY DIFFRACTIONr_mcangle_other2.9054.0886169
X-RAY DIFFRACTIONr_scbond_it3.2192.6675319
X-RAY DIFFRACTIONr_scbond_other3.2192.6675319
X-RAY DIFFRACTIONr_scangle_it4.7934.747713
X-RAY DIFFRACTIONr_scangle_other4.7934.747714
X-RAY DIFFRACTIONr_lrange_it6.28423.66111743
X-RAY DIFFRACTIONr_lrange_other6.28423.66311744
X-RAY DIFFRACTIONr_ncsr_local_group_10.0790.0520880
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.078550.05008
12AX-RAY DIFFRACTIONLocal ncs0.078550.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.970.34030.2677964X-RAY DIFFRACTION99.9522
1.97-2.0240.2544340.247801X-RAY DIFFRACTION99.9757
2.024-2.0820.2753700.2237609X-RAY DIFFRACTION100
2.082-2.1460.2554070.2017407X-RAY DIFFRACTION100
2.146-2.2170.2233910.1857109X-RAY DIFFRACTION100
2.217-2.2940.1983440.1746944X-RAY DIFFRACTION100
2.294-2.3810.2043330.1696722X-RAY DIFFRACTION100
2.381-2.4780.2223480.186427X-RAY DIFFRACTION100
2.478-2.5880.2173480.1756203X-RAY DIFFRACTION100
2.588-2.7140.1963170.1735929X-RAY DIFFRACTION99.984
2.714-2.860.2153040.1745650X-RAY DIFFRACTION100
2.86-3.0340.2092640.1825361X-RAY DIFFRACTION100
3.034-3.2420.2222760.2055025X-RAY DIFFRACTION100
3.242-3.5010.222600.2014746X-RAY DIFFRACTION100
3.501-3.8340.222250.1814373X-RAY DIFFRACTION100
3.834-4.2850.1661860.1453957X-RAY DIFFRACTION100
4.285-4.9430.1432050.1373528X-RAY DIFFRACTION100
4.943-6.0440.2161550.1673021X-RAY DIFFRACTION100
6.044-8.5060.1911190.1742384X-RAY DIFFRACTION100
8.506-60.660.232700.1711439X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.52830.46370.05961.01330.42410.66110.0356-0.04990.03210.121-0.0235-0.0314-0.00460.0918-0.01220.0328-0.0036-0.0020.03230.0080.016516.7751-5.9308-2.1392
20.1150.17250.44570.27920.72691.9419-0.00080.0137-0.02470.03120.0411-0.00520.17470.1393-0.04040.19520.0577-0.01220.1026-0.01430.096612.1491-44.6266-56.919
Refinement TLS groupSelection: ALL

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