PDB-8r75: Polysaccharide lyase BtPL33HA (BT4410) Apo form 1

ID or keywords:

Entry

Database: PDB / ID: 8r75

Title

Polysaccharide lyase BtPL33HA (BT4410) Apo form 1

Components

Heparinase

Keywords

LYASE / Polysaccharide lyase / glycosaminoglycan / Hyaluronic acid / conformational change

Function / homology

Heparinase II/III-like / Heparinase II/III-like, C-terminal / Chondroitin AC/alginate lyase / cell envelope / lyase activity / metal ion binding / Heparinase II/III-like C-terminal domain-containing protein

Function and homology information

Biological species

Bacteroides thetaiotaomicron VPI-5482 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

Cartmell, A.

Funding support

United Kingdom, 2items

Citation

Journal: 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. ...

History

Deposition	Nov 23, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 4, 2024	Provider: repository / Type: Initial release
Revision 1.1	Feb 26, 2025	Group: 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 1.2	Mar 5, 2025	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8r75.cif.gz	1.2 MB	Display	PDBx/mmCIF format
PDB format	pdb8r75.ent.gz	801.6 KB	Display	PDB format
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Validation report

Summary document	8r75_validation.pdf.gz	443.9 KB	Display	wwPDB validaton report
Full document	8r75_full_validation.pdf.gz	460.9 KB	Display
Data in XML	8r75_validation.xml.gz	48.4 KB	Display
Data in CIF	8r75_validation.cif.gz	62.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/r7/8r75 ftp://data.pdbj.org/pub/pdb/validation_reports/r7/8r75	HTTPS FTP

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Related structure data

Related structure data	8r6zC 8r70C 8r71C 8r72C 8r73C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Heparinase

B: Heparinase

hetero molecules

146 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Heparinase

hetero molecules

defined by author
Evidence: SAXS, Head to head dimer
73 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Heparinase

hetero molecules

defined by author
73 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	74.370, 101.580, 161.830
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P22₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A

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: A / Label asym-ID: A / Auth seq-ID: 28 - 643 / Label seq-ID: 20 - 635

Dom-ID
1
2

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

#1: Protein	Heparinase Mass: 72892.680 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.: 2 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.1 Å³/Da / Density % sol: 41.33 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 20 % PEG 3350 0.2 M Na/K Tartrate 20 mg/ml protein

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.6533 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 19, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.6533 Å / Relative weight: 1
Reflection	Resolution: 2.7→48.61 Å / Num. obs: 34414 / % possible obs: 100 % / Redundancy: 31.4 % / CC_1/2: 0.999 / Net I/σ(I): 15.8
Reflection shell	Resolution: 2.7→2.83 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4486 / CC_1/2: 0.735

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0419	refinement
xia2		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.7→48.506 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.91 / WR_factor R_free: 0.272 / WR_factor R_work: 0.175 / SU B: 41.438 / SU ML: 0.367 / Average fsc free: 0.9389 / Average fsc work: 0.9709 / Cross valid method: FREE R-VALUE / ESU R Free: 0.42
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2782	1694	4.922 %
R_work	0.18	32720	-
all	0.185	-	-
obs	-	34414	99.922 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 90.08 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.139 Å²	0 Å²	-0 Å²
2-	-	-3.339 Å²	-0 Å²
3-	-	-	4.478 Å²

Refinement step

Cycle: LAST / Resolution: 2.7→48.506 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9885	0	2	2	9889

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.012	10127
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	9445
X-RAY DIFFRACTION	r_angle_refined_deg	2.1	1.822	13706
X-RAY DIFFRACTION	r_angle_other_deg	0.691	1.772	21733
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.828	5	1225
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	9.802	5	54
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.821	10	1764
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.166	10	492
X-RAY DIFFRACTION	r_chiral_restr	0.097	0.2	1437
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	12087
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2449
X-RAY DIFFRACTION	r_nbd_refined	0.23	0.2	2103
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.204	0.2	8759
X-RAY DIFFRACTION	r_nbtor_refined	0.193	0.2	4908
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.087	0.2	5610
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.185	0.2	183
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.102	0.2	5
X-RAY DIFFRACTION	r_metal_ion_refined	0.09	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.195	0.2	23
X-RAY DIFFRACTION	r_nbd_other	0.196	0.2	127
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.174	0.2	10
X-RAY DIFFRACTION	r_mcbond_it	7.486	6.478	4909
X-RAY DIFFRACTION	r_mcbond_other	7.486	6.478	4909
X-RAY DIFFRACTION	r_mcangle_it	9.909	11.65	6131
X-RAY DIFFRACTION	r_mcangle_other	9.91	11.65	6132
X-RAY DIFFRACTION	r_scbond_it	8.345	6.893	5218
X-RAY DIFFRACTION	r_scbond_other	8.345	6.894	5219
X-RAY DIFFRACTION	r_scangle_it	11.262	12.475	7575
X-RAY DIFFRACTION	r_scangle_other	11.261	12.475	7576
X-RAY DIFFRACTION	r_lrange_it	12.716	64.714	11338
X-RAY DIFFRACTION	r_lrange_other	12.717	64.715	11339
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.099	0.05	20342

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.09866	0.05008
1	2	A	X-RAY DIFFRACTION	Local ncs	0.09866	0.05008

LS refinement shell

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

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.7-2.77	0.346	108	0.281	2381	0.283	2489	0.911	0.938	100	0.281
2.77-2.846	0.368	123	0.276	2333	0.281	2456	0.907	0.942	100	0.27
2.846-2.928	0.327	127	0.23	2227	0.235	2355	0.917	0.96	99.9575	0.219
2.928-3.018	0.353	105	0.218	2194	0.224	2299	0.914	0.966	100	0.204
3.018-3.116	0.373	92	0.237	2141	0.243	2233	0.909	0.959	100	0.219
3.116-3.225	0.351	108	0.209	2079	0.216	2188	0.927	0.97	99.9543	0.188
3.225-3.346	0.351	108	0.199	1964	0.207	2073	0.918	0.971	99.9518	0.176
3.346-3.482	0.282	94	0.172	1927	0.178	2023	0.947	0.981	99.9011	0.154
3.482-3.636	0.265	107	0.166	1836	0.171	1945	0.954	0.981	99.8972	0.147
3.636-3.812	0.267	103	0.17	1757	0.175	1863	0.954	0.981	99.839	0.156
3.812-4.017	0.27	74	0.162	1702	0.167	1777	0.95	0.982	99.9437	0.152
4.017-4.259	0.274	91	0.162	1597	0.169	1690	0.954	0.982	99.8817	0.156
4.259-4.551	0.197	83	0.142	1497	0.145	1580	0.972	0.987	100	0.142
4.551-4.912	0.22	80	0.131	1412	0.136	1493	0.972	0.989	99.933	0.136
4.912-5.375	0.235	68	0.133	1305	0.138	1374	0.972	0.99	99.9272	0.138
5.375-6	0.269	55	0.162	1209	0.166	1265	0.967	0.987	99.9209	0.17
6-6.911	0.311	64	0.189	1043	0.196	1109	0.953	0.98	99.8197	0.198
6.911-8.422	0.235	46	0.153	921	0.157	967	0.963	0.985	100	0.173
8.422-11.734	0.311	34	0.198	732	0.204	766	0.965	0.983	100	0.216
11.734-48.506	0.321	24	0.304	463	0.305	487	0.958	0.953	100	0.335

Refinement TLS params.

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

ID	L11 (°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)
1	1.0108	-0.9699	0.3754	2.217	-0.6268	0.2609	-0.1484	-0.0375	0.1182	-0.1484	0.2083	0.0442	-0.0416	-0.1376	-0.0599	0.1213	0.0065	0.009	0.3222	-0.0001	0.163	-0.9383	-27.0722	20.4095
2	0.2372	0.5901	0.3043	2.08	1.3193	1.0078	0.0439	0.0466	-0.0171	0.1912	-0.1023	0.1333	0.1523	-0.152	0.0584	0.0303	0.0097	0.03	0.2445	0.0643	0.2126	-21.7031	-37.4865	47.4692

Refinement TLS group

Selection: ALL

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