PDB-7dmk: PL6 alginate lyase BcAlyPL6

ID or keywords:

Entry

Database: PDB / ID: 7dmk

Title

PL6 alginate lyase BcAlyPL6

Components

BcAlyPL6

Keywords

LYASE / BcAlyPL6 / alginate lyas / PL6 / human gut microbe

Function / homology

raffinose alpha-galactosidase activity / PL-6 family / Chondroitinase B / Parallel beta-helix repeat / Parallel beta-helix repeats / Pectin lyase fold / Pectin lyase fold/virulence factor / MALONATE ION / Uncharacterized protein

Function and homology information

Biological species

Bacteroides clarus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.213 Å

Authors

Dong, S. / Wang, B. / Ma, X.Q. / Li, F.L. / Feng, Y.G.

Citation

Journal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Structural basis for the exolytic activity of polysaccharide lyase family 6 alginate lyase BcAlyPL6 from human gut microbe Bacteroides clarus.
Authors: Wang, B. / Dong, S. / Li, F.L. / Ma, X.Q.

History

Deposition	Dec 4, 2020	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Oct 6, 2021	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7dmk.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb7dmk.ent.gz	949.9 KB	Display	PDB format
PDBx/mmJSON format	7dmk.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7dmk_validation.pdf.gz	3.1 MB	Display	wwPDB validaton report
Full document	7dmk_full_validation.pdf.gz	3.1 MB	Display
Data in XML	7dmk_validation.xml.gz	107.3 KB	Display
Data in CIF	7dmk_validation.cif.gz	154.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dm/7dmk ftp://data.pdbj.org/pub/pdb/validation_reports/dm/7dmk	HTTPS FTP

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Related structure data

Related structure data	5gkdS S: Starting model for refinement
Similar structure data	7dmk-3 7dmk-2 4lgd-2 5jmq-1 3mqk-d 3a37-d 4ikp-2 6a5a-d 7dmk-4 5u4x-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) 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

Related structure data

5gkdS

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: BcAlyPL6

B: BcAlyPL6

C: BcAlyPL6

D: BcAlyPL6

hetero molecules

330 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: BcAlyPL6

hetero molecules

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

2

B: BcAlyPL6

hetero molecules

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

3

C: BcAlyPL6

hetero molecules

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

4

D: BcAlyPL6

hetero molecules

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

Unit cell

Length a, b, c (Å)	83.688, 97.693, 103.561
Angle α, β, γ (deg.)	76.560, 86.450, 88.690
Int Tables number	1
Space group name H-M	P1

#1: Protein	BcAlyPL6 Mass: 82389.891 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides clarus (bacteria) / Gene: B5F24_03600 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1Y4JW59
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-MLI / MALONATE ION Mass: 102.046 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₂O₄ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1413 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.49 Å³/Da / Density % sol: 50.68 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.7 / Details: 0.2 M sodium malonate, 12% (w/v) PEG 3350, pH 5.7

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL19U1 / Wavelength: 0.979 Å

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 2, 2018

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.979 Å / Relative weight: 1

Reflection

Resolution: 2.2→50 Å / Num. obs: 148419 / % possible obs: 93.8 % / Redundancy: 3.6 % / B_iso Wilson estimate: 30.26 Å² / R_merge(I) obs: 0.067 / R_pim(I) all: 0.041 / R_rim(I) all: 0.079 / Χ²: 0.853 / Net I/σ(I): 7.6

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.22-2.26	3.6	0.515	7585	0.899	0.319	0.608	1.274	95.7
2.26-2.3	3.6	0.465	7504	0.887	0.284	0.546	0.919	96.1
2.3-2.34	3.5	0.381	7647	0.906	0.234	0.448	0.9	95.9
2.34-2.39	3.5	0.346	7539	0.917	0.212	0.406	0.919	95
2.39-2.44	3.5	0.304	7388	0.931	0.185	0.357	0.876	93.3
2.44-2.5	3.5	0.282	6822	0.933	0.173	0.332	0.891	86.3
2.5-2.56	3.6	0.264	7400	0.939	0.161	0.31	0.91	93.8
2.56-2.63	3.6	0.221	7655	0.959	0.133	0.259	0.894	97.1
2.63-2.71	3.6	0.206	7691	0.961	0.125	0.241	1.009	96.3
2.71-2.8	3.7	0.158	7532	0.977	0.095	0.185	0.896	95.6
2.8-2.9	3.7	0.128	7575	0.982	0.078	0.15	0.88	95.5
2.9-3.01	3.6	0.104	7453	0.987	0.063	0.121	0.865	94.7
3.01-3.15	3.6	0.08	7306	0.99	0.048	0.094	0.832	92.3
3.15-3.32	3.6	0.063	6814	0.993	0.038	0.073	0.845	86.3
3.32-3.52	3.7	0.054	7708	0.991	0.033	0.063	0.899	97.3
3.52-3.8	3.7	0.04	7665	0.996	0.024	0.047	0.823	96.7
3.8-4.18	3.7	0.035	7489	0.996	0.021	0.041	0.775	94.9
4.18-4.78	3.6	0.031	6911	0.996	0.019	0.036	0.691	87.4
4.78-6.02	3.7	0.027	7521	0.997	0.017	0.032	0.524	95
6.02-50	3.8	0.027	7214	0.996	0.016	0.032	0.454	91.2

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Processing

Software

Name	Version	Classification
HKL-3000		data scaling
PHENIX	1.13_2998	refinement
PDB_EXTRACT	3.25	data extraction
HKL-3000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5GKD

5gkd

Resolution: 2.213→49.42 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 23.1 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2151	6504	4.81 %
R_work	0.1665	128665	-
obs	0.1688	135169	85.16 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 102.23 Å² / B_iso mean: 36.2722 Å² / B_iso min: 15.87 Å²

Refinement step

Cycle: final / Resolution: 2.213→49.42 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	22688	0	32	1413	24133
B_iso mean	-	-	38.85	37.4	-
Num. residues	-	-	-	-	2924

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
2.2134-2.2385	0.3232	145	0.2244	2688	54
2.2385-2.2649	0.2829	147	0.2163	3217	63
2.2649-2.2925	0.2621	151	0.2013	3386	68
2.2925-2.3215	0.2679	192	0.2002	3473	68
2.3215-2.3521	0.2753	171	0.1948	3550	70
2.3521-2.3843	0.2452	179	0.1964	3605	71
2.3843-2.4183	0.2717	170	0.1967	3718	74
2.4183-2.4544	0.2854	199	0.2056	3698	73
2.4544-2.4928	0.2538	193	0.2078	3553	71
2.4928-2.5336	0.2898	198	0.2042	3947	78
2.5336-2.5773	0.2535	230	0.2032	4514	90
2.5773-2.6242	0.2712	245	0.1987	4620	92
2.6242-2.6747	0.2579	264	0.2009	4740	95
2.6747-2.7293	0.2768	249	0.1956	4856	95
2.7293-2.7886	0.2357	229	0.1904	4821	95
2.7886-2.8535	0.2651	229	0.1889	4784	96
2.8535-2.9248	0.2603	248	0.1854	4799	96
2.9248-3.0039	0.2262	253	0.1861	4733	94
3.0039-3.0923	0.2371	232	0.1802	4723	93
3.0923-3.1921	0.2243	235	0.1676	4515	90
3.1921-3.3061	0.2163	233	0.166	4253	85
3.3061-3.4385	0.193	269	0.1623	4887	97
3.4385-3.5949	0.2022	248	0.1539	4884	97
3.5949-3.7844	0.1995	231	0.15	4897	96
3.7844-4.0214	0.1974	228	0.1453	4799	95
4.0214-4.3317	0.173	274	0.1368	4645	93
4.3317-4.7673	0.1471	191	0.1201	4301	85
4.7673-5.4564	0.18	236	0.1403	4759	94
5.4564-6.8715	0.1886	248	0.1698	4767	95
6.8715-49.42	0.1858	187	0.1598	4533	89

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	3.6993	-2.2414	-2.7566	3	0.5293	4.0186	0.1114	0.1877	0.0034	-0.7148	-0.0512	-0.1151	-0.0348	0.1147	-0.0484	0.3097	-0.0209	-0.021	0.2285	-0.0086	0.1832	-77.545	-25.109	-74.015
2	0.8057	-0.1878	-0.0704	2.1837	-0.1779	2.0434	-0.0022	0.1888	0.1646	-0.2677	-0.0119	0.0507	-0.5662	-0.0343	0.0381	0.3963	0.0239	0.001	0.2099	0.0492	0.2477	-28.956	-35.501	4.498
3	0.6853	0.1081	-0.0215	1.0951	-0.3518	1.7031	0.0331	-0.0004	0.033	0.1361	0.0328	0.1003	-0.0639	-0.0965	-0.0685	0.2217	0.0038	0.0243	0.176	-0.0068	0.3019	-31.223	-51.644	31.488
4	1.2963	-0.8499	-0.2127	2.8339	1.2304	1.7373	0.0647	0.3087	-0.094	-0.3602	-0.0018	0.1786	0.197	-0.0903	-0.0516	0.3438	-0.0322	-0.0603	0.3388	0.0364	0.2227	-29.539	-72.562	-8.229
5	1.6441	-0.599	0.1673	2.799	-0.4799	2.0614	0.0396	0.0851	-0.1439	-0.2627	-0.0016	-0.0924	0.2005	0.1249	-0.047	0.2094	0.0188	0.018	0.181	-0.0197	0.1998	-18.165	-74.925	6.693
6	1.9787	0.466	0.9873	0.5164	-0.2338	0.9834	0.1826	-0.0989	-0.2034	-0.0371	-0.0863	0.0031	0.3039	-0.0273	-0.0788	0.284	-0.0074	0.0166	0.1743	0.0002	0.1961	-19.747	-86.1	18.739
7	0.822	0.1709	0.2867	2.2635	-0.0179	2.2972	0.0095	0.2953	0.0557	-0.3479	-0.0478	0.0229	-0.1083	0.2112	0.0279	0.2214	0.039	-0.0069	0.3582	0.0302	0.1689	-69.887	-68.344	-19.79
8	0.9843	0.2148	0.163	3.099	-0.7018	2.664	0.0554	0.1555	-0.0429	-0.1111	-0.0566	-0.0475	0.1427	0.2742	-0.0064	0.1386	0.0387	-0.0026	0.2763	-0.0336	0.1676	-66.401	-85.493	-0.426
9	1.5408	-0.036	0.1261	1.817	-1.1073	1.4705	0.0556	0.1062	-0.0254	-0.0082	-0.143	-0.2676	0.0924	0.3843	0.0975	0.2153	0.0578	-0.0109	0.3679	-0.0633	0.2412	-59.092	-93.316	7.317
10	0.8506	-0.1916	-0.7558	1.9193	1.4928	3.1198	0.0806	0.1146	0.419	0.1147	0.0479	-0.2172	-0.6158	0.1695	-0.1972	0.4373	-0.0683	-0.0053	0.2581	0.0817	0.3326	-66.97	-42.157	13.841
11	0.3704	-0.0923	-0.1198	2.7374	2.0436	4.511	-0.0382	0.0371	0.0388	-0.0266	-0.0879	0.2435	-0.2643	-0.1409	0.1261	0.1596	-0.0063	0.0086	0.1916	0.0227	0.2047	-75.882	-57.881	17.329
12	1.4376	0.7747	0.4701	0.4601	0.1285	0.2274	0.108	-0.1158	-0.023	0.1345	-0.0745	0.0277	0.0412	-0.0556	-0.0741	0.295	0.002	0.0011	0.2548	0.0253	0.2348	-75.253	-66.342	32.357
13	0.7081	-0.1214	0.1524	1.9368	-0.0729	2.3311	0.108	-0.244	-0.1847	0.2889	0.0058	0.1099	0.5326	-0.3159	-0.0827	0.3301	-0.1036	-0.0357	0.2886	0.0658	0.292	-34.884	-49.648	-43.519
14	4.1215	-0.9458	0.3649	1.1323	-0.2214	1.9839	0.0828	0.058	-0.0714	-0.1391	-0.0013	0.109	0.0421	-0.1356	-0.0813	0.2335	-0.0386	-0.0341	0.1398	0.0123	0.2358	-36.065	-34.016	-70.944
15	0.2957	0.793	0.0929	2.2965	0.3952	0.1479	0.216	-0.2932	0.0434	0.7011	-0.2492	0.3888	0.0664	-0.3106	0.0839	0.4886	-0.0266	0.1636	0.5785	-0.0112	0.4347	-41.919	-24.689	-29.91
16	1.0133	0.5475	-0.1895	1.823	-0.3836	0.8754	0.115	-0.1728	0.0145	0.4286	-0.0432	0.0471	-0.1522	0.0014	-0.0654	0.2666	0.0137	-0.0156	0.2074	-0.019	0.1971	-23.21	-11.473	-39.08
17	4.0809	-3.8882	-1.2114	6.3859	1.0134	1.8329	0.1942	0.0898	0.0219	-0.28	-0.213	0.1916	-0.2587	-0.1568	-0.0261	0.2699	-0.0132	0.0065	0.1771	0.0317	0.1988	-24.825	3.514	-53.222
18	0.9403	0.0585	0.0153	1.7346	0.4791	1.9011	-0.0448	-0.2933	-0.1052	0.3836	0.0836	-0.0074	0.305	0.1226	-0.0356	0.2823	0.0299	-0.0175	0.3308	0.0567	0.1783	-70.039	-22.348	-16.171
19	1.473	-0.2197	-0.0868	1.8105	-0.0345	1.3547	0.0362	-0.1603	-0.0036	-0.0711	0.0144	-0.083	-0.1056	0.1819	-0.0521	0.2219	-0.0271	0.0127	0.2644	-0.0211	0.1763	-68.16	-5.353	-36.017
20	2.0169	0.122	-0.6399	1.3503	-0.6751	1.5689	0.011	-0.0515	0.1053	-0.1542	-0.0366	-0.2633	-0.1218	0.2402	0.0222	0.2796	-0.036	0.0322	0.2885	-0.0651	0.1954	-61.591	1.937	-45.087
21	0.9848	-0.0852	0.2777	0.6252	0.0133	1.4063	0.0283	-0.0871	-0.1807	0.0419	-0.01	-0.0182	0.2726	0.082	-0.0219	0.2086	-0.0055	0.0086	0.1873	0.0172	0.2342	-78.086	-35.95	-53.905

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN B AND RESID 694:747 )	B	694 - 747
2	X-RAY DIFFRACTION	2	( CHAIN C AND RESID 13:207 )	C	13 - 207
3	X-RAY DIFFRACTION	3	( CHAIN C AND RESID 208:402 )	C	208 - 402
4	X-RAY DIFFRACTION	4	( CHAIN C AND RESID 403:526 )	C	403 - 526
5	X-RAY DIFFRACTION	5	( CHAIN C AND RESID 527:649 )	C	527 - 649
6	X-RAY DIFFRACTION	6	( CHAIN C AND RESID 650:746 )	C	650 - 746
7	X-RAY DIFFRACTION	7	( CHAIN D AND RESID 14:207 )	D	14 - 207
8	X-RAY DIFFRACTION	8	( CHAIN D AND RESID 208:334 )	D	208 - 334
9	X-RAY DIFFRACTION	9	( CHAIN D AND RESID 335:411 )	D	335 - 411
10	X-RAY DIFFRACTION	10	( CHAIN D AND RESID 412:526 )	D	412 - 526
11	X-RAY DIFFRACTION	11	( CHAIN D AND RESID 527:629 )	D	527 - 629
12	X-RAY DIFFRACTION	12	( CHAIN D AND RESID 630:746 )	D	630 - 746
13	X-RAY DIFFRACTION	13	( CHAIN A AND RESID 11:270 )	A	11 - 270
14	X-RAY DIFFRACTION	14	( CHAIN A AND RESID 271:402 )	A	271 - 402
15	X-RAY DIFFRACTION	15	( CHAIN A AND RESID 403:450 )	A	403 - 450
16	X-RAY DIFFRACTION	16	( CHAIN A AND RESID 451:693 )	A	451 - 693
17	X-RAY DIFFRACTION	17	( CHAIN A AND RESID 694:747 )	A	694 - 747
18	X-RAY DIFFRACTION	18	( CHAIN B AND RESID 13:207 )	B	13 - 207
19	X-RAY DIFFRACTION	19	( CHAIN B AND RESID 208:334 )	B	208 - 334
20	X-RAY DIFFRACTION	20	( CHAIN B AND RESID 335:411 )	B	335 - 411
21	X-RAY DIFFRACTION	21	( CHAIN B AND RESID 412:693 )	B	412 - 693

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Yorodumi