PDB-6qps: Structural characterization of a mannuronic acid specific polysac...

ID or keywords:

Entry

Database: PDB / ID: 6qps

Title

Structural characterization of a mannuronic acid specific polysaccharide family 6 lyase enzyme from human gut microbiota

Components

Polysaccharide Lyase Family 6

Keywords

LYASE / Native enzyme

Function / homology

PL-6 family / Chondroitinase B / alpha-galactosidase activity / Pectin lyase fold / Pectin lyase fold/virulence factor / metal ion binding / ACETATE ION / Poly(Beta-D-mannuronate) lyase

Function and homology information

Biological species

Bacteroides cellulosilyticus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.287 Å

Authors

Fredslund, F. / Stender, E.G.P. / Svensson, B. / Welner, D.H.

Funding support

Denmark, 1items

Citation

Journal: J.Biol.Chem. / Year: 2019
Title: Structural and functional aspects of mannuronic acid-specific PL6 alginate lyase from the human gut microbeBacteroides cellulosilyticus.
Authors: Stender, E.G.P. / Dybdahl Andersen, C. / Fredslund, F. / Holck, J. / Solberg, A. / Teze, D. / Peters, G.H.J. / Christensen, B.E. / Aachmann, F.L. / Welner, D.H. / Svensson, B.

History

Deposition	Feb 14, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 25, 2019	Provider: repository / Type: Initial release
Revision 1.1	Oct 2, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	Dec 4, 2019	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3	Jan 24, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6qps.cif.gz	550.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6qps.ent.gz	460.1 KB	Display	PDB format
PDBx/mmJSON format	6qps.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6qps_validation.pdf.gz	451.4 KB	Display	wwPDB validaton report
Full document	6qps_full_validation.pdf.gz	458.5 KB	Display
Data in XML	6qps_validation.xml.gz	46.1 KB	Display
Data in CIF	6qps_validation.cif.gz	72.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qp/6qps ftp://data.pdbj.org/pub/pdb/validation_reports/qp/6qps	HTTPS FTP

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Related structure data

Related structure data	5gkdS S: Starting model for refinement
Similar structure data	4j28-2 2xib-2 4pct-2 2np6-2 2wvv-1 2wvs-3 6iyt-1 4j27-1 2wvu-3 6iyt-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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: Polysaccharide Lyase Family 6

B: Polysaccharide Lyase Family 6

hetero molecules

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

1

A: Polysaccharide Lyase Family 6

hetero molecules

defined by author
Evidence: gel filtration
53 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Polysaccharide Lyase Family 6

hetero molecules

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

Unit cell

Length a, b, c (Å)	58.623, 129.951, 66.995
Angle α, β, γ (deg.)	90.00, 113.90, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Polysaccharide Lyase Family 6 Mass: 52889.379 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides cellulosilyticus (bacteria) Gene: PL6 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E2NM07
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1264 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.21 Å³/Da / Density % sol: 44.23 %
Crystal grow	Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2 M calcium acetate hydrate, 0.1 M Tris-HCl, 20 % (w/v) PEG 3000 Temp details: Room temperature

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873127 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 12, 2018 Details: Focusing mirrors: one pair of (300x40x15) mm3 long Pt coated Si mirror, 260mm usable, in a Kirkpatrick-Baez geometry
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.873127 Å / Relative weight: 1
Reflection	Resolution: 1.287→55.4 Å / Num. obs: 230084 / % possible obs: 99.65 % / Redundancy: 6.6 % / CC_1/2: 0.998 / Net I/σ(I): 7.23
Reflection shell	Resolution: 1.287→1.333 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 1.69 / Num. unique obs: 22263 / CC_1/2: 0.535 / % possible all: 96.59

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Processing

Software

Name	Version	Classification
PHENIX	(1.14_3260: ???)	refinement
DIALS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5GKD

5gkd

Resolution: 1.287→55.4 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 17.88

	R_factor	Num. reflection	% reflection
R_free	0.1749	11301	4.91 %
R_work	0.1587	-	-
obs	0.1595	230060	99.61 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.287→55.4 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7116	0	18	1264	8398

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	7593
X-RAY DIFFRACTION	f_angle_d	1.088	10297
X-RAY DIFFRACTION	f_dihedral_angle_d	3.028	6094
X-RAY DIFFRACTION	f_chiral_restr	0.092	1073
X-RAY DIFFRACTION	f_plane_restr	0.007	1381

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.2869-1.3015	0.2935	311	0.2647	6500	X-RAY DIFFRACTION	89
1.3015-1.3168	0.2488	372	0.2594	7314	X-RAY DIFFRACTION	100
1.3168-1.3329	0.2949	420	0.2587	7259	X-RAY DIFFRACTION	100
1.3329-1.3498	0.2625	368	0.2587	7289	X-RAY DIFFRACTION	100
1.3498-1.3675	0.2748	361	0.2512	7363	X-RAY DIFFRACTION	100
1.3675-1.3863	0.2516	367	0.2439	7267	X-RAY DIFFRACTION	100
1.3863-1.4061	0.2382	392	0.2325	7293	X-RAY DIFFRACTION	100
1.4061-1.427	0.2333	392	0.2267	7318	X-RAY DIFFRACTION	100
1.427-1.4494	0.2434	313	0.2151	7345	X-RAY DIFFRACTION	100
1.4494-1.4731	0.2278	357	0.2018	7300	X-RAY DIFFRACTION	100
1.4731-1.4985	0.2079	421	0.1919	7326	X-RAY DIFFRACTION	100
1.4985-1.5258	0.2172	376	0.1919	7252	X-RAY DIFFRACTION	100
1.5258-1.5551	0.2111	346	0.1832	7391	X-RAY DIFFRACTION	100
1.5551-1.5869	0.1881	377	0.1761	7287	X-RAY DIFFRACTION	100
1.5869-1.6214	0.2026	345	0.1747	7335	X-RAY DIFFRACTION	100
1.6214-1.6591	0.1816	375	0.1741	7324	X-RAY DIFFRACTION	100
1.6591-1.7006	0.1998	363	0.1773	7316	X-RAY DIFFRACTION	100
1.7006-1.7466	0.2042	397	0.1703	7266	X-RAY DIFFRACTION	100
1.7466-1.798	0.1867	398	0.1666	7327	X-RAY DIFFRACTION	100
1.798-1.856	0.1797	402	0.1555	7299	X-RAY DIFFRACTION	100
1.856-1.9223	0.1694	391	0.1534	7317	X-RAY DIFFRACTION	100
1.9223-1.9993	0.1893	380	0.1558	7294	X-RAY DIFFRACTION	100
1.9993-2.0903	0.1502	348	0.1497	7402	X-RAY DIFFRACTION	100
2.0903-2.2005	0.1632	412	0.1404	7257	X-RAY DIFFRACTION	100
2.2005-2.3384	0.1459	402	0.1276	7306	X-RAY DIFFRACTION	100
2.3384-2.519	0.1432	349	0.1288	7356	X-RAY DIFFRACTION	100
2.519-2.7724	0.148	365	0.1342	7385	X-RAY DIFFRACTION	100
2.7724-3.1736	0.1505	380	0.135	7329	X-RAY DIFFRACTION	100
3.1736-3.9984	0.1459	406	0.1281	7336	X-RAY DIFFRACTION	100
3.9984-65.0584	0.1467	415	0.1395	7406	X-RAY DIFFRACTION	100

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	1.6028	-0.2083	-0.4524	1.1736	-0.3965	2.3796	0.1204	0.2127	0.1306	-0.1953	-0.0227	0.0832	-0.1358	-0.2039	-0.0846	0.1757	0.0407	-0.0119	0.1182	0.0355	0.1025	11.4028	90.2239	-13.0867
2	1.2266	-0.1304	-0.2626	1.2267	0.0079	1.7146	0.038	0.0212	0.0902	-0.0829	-0.0279	-0.1265	-0.1416	0.0724	-0.0184	0.1089	0.0114	0.0036	0.055	0.0126	0.0811	22.3211	86.5357	-3.8934
3	0.4152	-0.0653	-0.0793	0.3706	-0.0508	0.5662	0.0157	-0.0094	0.0362	-0.0349	-0.013	-0.0592	-0.0538	0.0385	-0.0059	0.0797	-0.0063	0.0064	0.0805	-0.0041	0.0843	27.3432	74.135	4.3201
4	0.6977	0.1144	0.1202	1.4412	0.4213	0.9134	-0.005	-0.0694	0.067	0.0447	0.0406	-0.1607	-0.0558	0.1102	-0.04	0.0539	-0.0001	-0.008	0.0846	-0.0048	0.0921	35.8748	66.193	17.9646
5	1.8762	-0.7557	-0.2619	2.3273	0.4645	2.3781	-0.1103	-0.1006	-0.0447	0.0478	0.0899	-0.1669	0.1244	0.1027	-0.0033	0.0714	0.0124	-0.0074	0.0865	0.0181	0.1314	39.7321	49.2793	18.6171
6	0.9047	-0.6766	0.412	1.7564	-0.7796	1.3987	0.0804	0.1059	-0.0285	-0.1309	-0.0873	0.012	0.0271	0.0361	-0.0217	0.1274	0.0104	0.0049	0.112	-0.0318	0.0977	25.2249	61.0507	-9.3907
7	1.5486	0.7981	-0.1161	2.0606	-0.5357	1.1978	0.0005	-0.0623	-0.0615	0.0543	-0.0587	-0.137	0.0295	0.1094	0.0643	0.102	0.0164	-0.0124	0.1005	0.0261	0.0786	27.4236	41.42	46.4396
8	2.1017	0.1167	-0.2759	1.6547	-0.2088	1.3189	-0.0317	-0.0804	0.0173	0.141	0.0133	0.0926	-0.026	-0.0828	0.0186	0.0913	0.0096	-0.013	0.0801	0.0123	0.0411	15.2504	48.4799	41.0626
9	0.3396	0.0113	-0.0453	0.6042	-0.1416	0.3716	0.001	-0.0215	-0.006	0.0506	0.0054	0.0424	0.0127	-0.0405	-0.0082	0.0606	-0.0034	-0.0018	0.074	-0.0006	0.0664	11.259	54.7807	27.6242
10	0.3392	-0.1517	-0.2994	0.9121	0.613	1.4005	0.0195	-0.007	0.0145	-0.0086	-0.0371	0.1318	-0.0491	-0.138	0.022	0.0477	0.0041	-0.0074	0.0876	0.0021	0.0775	2.8205	66.7869	17.3159
11	1.9043	-0.5986	0.273	2.7613	0.9548	2.3295	-0.0409	0.0062	0.0572	-0.096	-0.0269	0.1538	0.0192	-0.1647	0.0702	0.0837	-0.0074	-0.0252	0.1282	0.0117	0.0918	-0.2311	64.6798	1.0749
12	1.1997	-0.4998	1.442	1.0555	-0.6036	3.2522	0.1696	0.0374	-0.1653	-0.0373	-0.0028	0.1069	0.3201	0.086	-0.1679	0.1477	0.0037	-0.0244	0.0853	-0.0227	0.1399	13.3368	38.8769	17.2917

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 21 through 94 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 95 through 164 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 165 through 292 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 293 through 389 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 390 through 432 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 433 through 467 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 21 through 97 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 98 through 164 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 165 through 292 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 293 through 389 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 390 through 432 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 433 through 467 )

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