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- PDB-8r6z: Polysaccharide lyase BtPL33HA (BT4410) Apo form 2 -

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Basic information

Entry
Database: PDB / ID: 8r6z
TitlePolysaccharide lyase BtPL33HA (BT4410) Apo form 2
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 / 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: 2.03 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

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Assembly

Deposited unit
B: Heparinase
A: Heparinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,4524
Polymers147,3212
Non-polymers1312
Water5,999333
1
B: Heparinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7262
Polymers73,6611
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Heparinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7262
Polymers73,6611
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.529, 137.672, 202.506
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
11B
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ILE / End label comp-ID: ILE / Auth asym-ID: B / Label asym-ID: A / Auth seq-ID: 28 - 643 / Label seq-ID: 28 - 643

Dom-ID
1
2

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

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Components

#1: Protein Heparinase


Mass: 73660.547 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: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 333 / 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: 2.53 Å3/Da / Density % sol: 51.43 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 20 % PEG 6000 0.1M MES pH6.0 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: I24 / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.03→113.85 Å / Num. obs: 73386 / % possible obs: 90.8 % / Redundancy: 5.9 % / CC1/2: 0.99 / Net I/σ(I): 6.6
Reflection shellResolution: 2.03→2.17 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3670 / CC1/2: 0.503

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
autoPROCdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→113.85 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.902 / SU B: 12.234 / SU ML: 0.158 / Cross valid method: FREE R-VALUE / ESU R: 0.256 / ESU R Free: 0.217
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2505 3607 4.915 %
Rwork0.1912 69778 -
all0.194 --
obs-73385 75.003 %
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: 31.44 Å2
Baniso -1Baniso -2Baniso -3
1--0.995 Å20 Å2-0 Å2
2--0.136 Å2-0 Å2
3---0.859 Å2
Refinement stepCycle: LAST / Resolution: 2.03→113.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9816 0 2 333 10151
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01210065
X-RAY DIFFRACTIONr_bond_other_d0.0010.0169389
X-RAY DIFFRACTIONr_angle_refined_deg2.5391.82213624
X-RAY DIFFRACTIONr_angle_other_deg0.8171.77121606
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.53551219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg19.388553
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.952101753
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.34110488
X-RAY DIFFRACTIONr_chiral_restr0.1110.21430
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212015
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022429
X-RAY DIFFRACTIONr_nbd_refined0.2240.22101
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2010.29060
X-RAY DIFFRACTIONr_nbtor_refined0.1940.25018
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0970.25775
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2388
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0570.24
X-RAY DIFFRACTIONr_metal_ion_refined0.250.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2260.213
X-RAY DIFFRACTIONr_nbd_other0.2080.296
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2040.29
X-RAY DIFFRACTIONr_mcbond_it2.4951.9184882
X-RAY DIFFRACTIONr_mcbond_other2.491.9184882
X-RAY DIFFRACTIONr_mcangle_it3.5463.4346099
X-RAY DIFFRACTIONr_mcangle_other3.5463.4346100
X-RAY DIFFRACTIONr_scbond_it3.8562.2795183
X-RAY DIFFRACTIONr_scbond_other3.8562.285184
X-RAY DIFFRACTIONr_scangle_it5.7143.9987525
X-RAY DIFFRACTIONr_scangle_other5.7133.9987526
X-RAY DIFFRACTIONr_lrange_it6.73119.04911567
X-RAY DIFFRACTIONr_lrange_other6.72618.83211540
X-RAY DIFFRACTIONr_ncsr_local_group_10.110.0520197
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11BX-RAY DIFFRACTIONLocal ncs0.110150.05008
12BX-RAY DIFFRACTIONLocal ncs0.110150.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.0820.325250.27430X-RAY DIFFRACTION6.3627
2.082-2.1390.297870.2721687X-RAY DIFFRACTION25.2959
2.139-2.2010.3161350.2662884X-RAY DIFFRACTION44.9791
2.201-2.2690.2972110.2543627X-RAY DIFFRACTION58.1868
2.269-2.3430.311940.2264089X-RAY DIFFRACTION66.8488
2.343-2.4260.2672070.2094244X-RAY DIFFRACTION71.9877
2.426-2.5170.2592140.2174463X-RAY DIFFRACTION78.6183
2.517-2.620.2672440.2134841X-RAY DIFFRACTION88.3579
2.62-2.7360.2682800.2135044X-RAY DIFFRACTION96.0837
2.736-2.870.2662360.2125037X-RAY DIFFRACTION99.4718
2.87-3.0250.2722580.2044799X-RAY DIFFRACTION100
3.025-3.2080.2692270.2034549X-RAY DIFFRACTION99.9581
3.208-3.4290.2742280.1954290X-RAY DIFFRACTION100
3.429-3.7040.2332140.1893993X-RAY DIFFRACTION99.9287
3.704-4.0570.2341990.1613701X-RAY DIFFRACTION99.9231
4.057-4.5350.1981840.1453353X-RAY DIFFRACTION99.887
4.535-5.2350.231530.1492981X-RAY DIFFRACTION99.8407
5.235-6.4090.2531510.1862545X-RAY DIFFRACTION100
6.409-9.0490.189950.172033X-RAY DIFFRACTION99.7656
9.049-113.850.255650.2021188X-RAY DIFFRACTION99.3656
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)
10.51320.40770.12460.84210.3190.41690.0492-0.04170.03170.1051-0.033-0.04-0.01450.047-0.01620.03890.00990.00230.05260.01120.014716.8686-5.8921-2.1055
20.1229-0.13990.38140.1924-0.50721.39510.006-0.0148-0.0367-0.02560.0206-0.00890.1577-0.0728-0.02660.1975-0.0453-0.02150.09280.01670.100941.467924.1549-44.3614
Refinement TLS groupSelection: ALL

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