PDB-5nav: Crystal structure of the double mutant (Cys211Ser/Cys292Ser) 6-ph...

ID or keywords:

Entry

Database: PDB / ID: 5nav

Title

Crystal structure of the double mutant (Cys211Ser/Cys292Ser) 6-phospho-b-D-glucosidase from Lactobacillus plantarum

Components

Beta-galactosidase

Keywords

HYDROLASE / cysteine residue / glycosides / protein aggregation / reducing agent / solubility enhancer

Function / homology

Function and homology information

beta-glucosidase / carbohydrate catabolic process / beta-glucosidase activity / cytosol
Similarity search - Function

Biological species

Lactobacillus plantarum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Acebron, I. / Mancheno, J.M.

Citation

Journal: Biochim. Biophys. Acta / Year: 2017
Title: Structural basis of the substrate specificity and instability in solution of a glycosidase from Lactobacillus plantarum.
Authors: Acebron, I. / Plaza-Vinuesa, L. / de Las Rivas, B. / Munoz, R. / Cumella, J. / Sanchez-Sancho, F. / Mancheno, J.M.

History

Deposition	Feb 28, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 2, 2017	Provider: repository / Type: Initial release
Revision 1.1	Aug 9, 2017	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0	Jan 17, 2024	Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5nav.cif.gz	807.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5nav.ent.gz	669.8 KB	Display	PDB format
PDBx/mmJSON format	5nav.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5nav_validation.pdf.gz	479.7 KB	Display	wwPDB validaton report
Full document	5nav_full_validation.pdf.gz	514.1 KB	Display
Data in XML	5nav_validation.xml.gz	111.8 KB	Display
Data in CIF	5nav_validation.cif.gz	161.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/na/5nav ftp://data.pdbj.org/pub/pdb/validation_reports/na/5nav	HTTPS FTP

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Related structure data

Related structure data	5naqSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6ux0-d 7lo6-d 23462 7lok-d 3sua-d 6u0n-d 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: Beta-galactosidase

B: Beta-galactosidase

C: Beta-galactosidase

D: Beta-galactosidase

E: Beta-galactosidase

F: Beta-galactosidase

327 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration, Analytical gel filtration and ultracentrifugation reveal the presence of a large oligomer (hexamer).

Unit cell

Length a, b, c (Å)	196.740, 192.060, 105.840
Angle α, β, γ (deg.)	90.00, 102.39, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	B-763- HOH

#1: Protein	Beta-galactosidase / 6-phospho-b-d-glucosidase Mass: 54530.797 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus plantarum (bacteria) / Gene: bgl, lp_3629 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: F9ULH8, beta-glucosidase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1666 / 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: 2.98 Å³/Da / Density % sol: 58.79 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 20% (w/v) PEG 3350, 0.2 M sodium citrate and 50 mM spermidine

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 16, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8726 Å / Relative weight: 1
Reflection	Resolution: 2.3→38.42 Å / Num. obs: 169552 / % possible obs: 100 % / Redundancy: 3.8 % / B_iso Wilson estimate: 34.9 Å² / R_merge(I) obs: 0.113 / R_pim(I) all: 0.067 / R_sym value: 0.132 / Net I/σ(I): 8.7
Reflection shell	Resolution: 2.3→2.42 Å / Redundancy: 3.5 % / R_merge(I) obs: 0.569 / Num. unique obs: 24703 / R_pim(I) all: 0.353 / R_sym value: 0.672 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5NAQ

5naq

Resolution: 2.3→38.38 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.71

	R_factor	Num. reflection	% reflection
R_free	0.2057	8504	5.02 %
R_work	0.1627	-	-
obs	0.1648	169538	99.97 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.3→38.38 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	22380	0	0	1666	24046

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	23106
X-RAY DIFFRACTION	f_angle_d	0.979	31494
X-RAY DIFFRACTION	f_dihedral_angle_d	15.754	13284
X-RAY DIFFRACTION	f_chiral_restr	0.057	3210
X-RAY DIFFRACTION	f_plane_restr	0.007	4134

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 (%)
2.3-2.3261	0.2925	313	0.2357	5322	X-RAY DIFFRACTION	100
2.3261-2.3535	0.3203	282	0.2385	5373	X-RAY DIFFRACTION	100
2.3535-2.3822	0.2652	264	0.2271	5344	X-RAY DIFFRACTION	100
2.3822-2.4123	0.2974	289	0.2234	5379	X-RAY DIFFRACTION	100
2.4123-2.4441	0.2767	291	0.2124	5288	X-RAY DIFFRACTION	100
2.4441-2.4776	0.2445	270	0.2058	5328	X-RAY DIFFRACTION	100
2.4776-2.5129	0.255	275	0.2069	5409	X-RAY DIFFRACTION	100
2.5129-2.5504	0.2476	304	0.1984	5334	X-RAY DIFFRACTION	100
2.5504-2.5903	0.2668	273	0.1913	5386	X-RAY DIFFRACTION	100
2.5903-2.6327	0.2436	273	0.1959	5342	X-RAY DIFFRACTION	100
2.6327-2.6781	0.2569	278	0.2022	5342	X-RAY DIFFRACTION	100
2.6781-2.7268	0.2566	303	0.2002	5335	X-RAY DIFFRACTION	100
2.7268-2.7793	0.2444	281	0.1898	5384	X-RAY DIFFRACTION	100
2.7793-2.836	0.2378	292	0.1896	5319	X-RAY DIFFRACTION	100
2.836-2.8976	0.2283	283	0.1773	5386	X-RAY DIFFRACTION	100
2.8976-2.965	0.2218	275	0.1695	5399	X-RAY DIFFRACTION	100
2.965-3.0391	0.2378	296	0.174	5345	X-RAY DIFFRACTION	100
3.0391-3.1212	0.2423	282	0.1744	5372	X-RAY DIFFRACTION	100
3.1212-3.213	0.2059	301	0.1721	5346	X-RAY DIFFRACTION	100
3.213-3.3167	0.22	291	0.1674	5375	X-RAY DIFFRACTION	100
3.3167-3.4352	0.1917	282	0.1581	5341	X-RAY DIFFRACTION	100
3.4352-3.5726	0.2134	275	0.1559	5377	X-RAY DIFFRACTION	100
3.5726-3.7351	0.1761	242	0.1494	5396	X-RAY DIFFRACTION	100
3.7351-3.9318	0.1685	288	0.1398	5398	X-RAY DIFFRACTION	100
3.9318-4.1779	0.1653	255	0.1322	5393	X-RAY DIFFRACTION	100
4.1779-4.5	0.1387	298	0.1207	5362	X-RAY DIFFRACTION	100
4.5-4.952	0.1558	265	0.1208	5402	X-RAY DIFFRACTION	100
4.952-5.6666	0.1768	296	0.1385	5390	X-RAY DIFFRACTION	100
5.6666-7.1318	0.1995	283	0.153	5421	X-RAY DIFFRACTION	100
7.1318-38.3855	0.1553	304	0.1348	5446	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	1.0736	0.1538	-0.2759	0.8812	-0.0775	0.9912	0.0936	-0.1149	-0.0232	0.1284	-0.0509	0.0081	-0.1437	-0.1455	-0.0317	0.2473	-0.0354	0.0277	0.2008	-0.0232	0.1289	-31.5992	-43.8607	26.5716
2	0.8641	-0.0388	-0.3808	1.1981	-0.0751	1.3922	0.0457	0.0432	-0.0479	-0.0023	-0.0062	-0.1743	-0.1572	0.0229	-0.0318	0.227	-0.0511	0.0259	0.2538	-0.0116	0.1789	-15.1576	-40.9095	11.4718
3	2.3382	0.3475	-0.2115	0.3675	-0.2625	1.1032	0.077	0.013	-0.5119	0.0845	-0.0501	-0.1227	0.1625	-0.0194	-0.0193	0.2216	-0.018	-0.0067	0.1892	-0.0386	0.2995	-21.8978	-61.9108	22.7029
4	1.5034	0.2355	0.4639	0.494	0.3488	1.3814	0.0544	-0.1418	-0.0138	-0.0511	0.0204	0.0276	0.0348	-0.0934	-0.0616	0.3405	0.0143	-0.0523	0.159	0.0317	0.2126	-34.2751	10.3048	37.9877
5	1.0275	0.0838	0.591	0.2524	0.5999	1.5173	-0.0189	0.2046	0.1135	-0.1555	0.0781	0.0312	-0.3069	0.3437	-0.0948	0.3799	-0.0466	-0.0276	0.2515	0.05	0.2696	-16.1259	21.426	30.703
6	3.2415	0.1414	2.4403	1.3212	-0.0758	3.4506	0.2565	0.2907	-0.2584	-0.2309	0.0174	-0.048	0.1349	0.0502	-0.2801	0.3497	0.0938	-0.0016	0.2639	-0.0374	0.2348	-22.2891	5.1716	20.839
7	1.921	0.142	0.5606	1.0314	0.247	0.8435	0.0302	0.255	-0.1173	-0.193	0.0659	-0.0123	0.1414	0.1385	-0.0862	0.4313	0.0689	-0.0354	0.2471	-0.004	0.2376	-28.6931	1.7753	20.0288
8	1.4067	-0.1943	-0.1672	0.7202	0.2452	0.7642	-0.114	0.064	0.1138	-0.0875	0.0395	0.0993	-0.1261	-0.0959	0.0746	0.2732	0.0845	0.0193	0.2376	0.0012	0.1754	-59.2454	-30.9501	63.5754
9	1.0262	0.0489	-0.0297	0.5107	0.062	0.6107	-0.1233	-0.1865	-0.0739	0.0544	0.0696	-0.0352	0.0367	0.0458	0.0658	0.3119	0.1016	0.0842	0.3199	0.0314	0.1858	-43.5574	-43.0412	68.1915
10	1.3311	0.1066	-1.0797	1.2776	0.3833	2.2547	0.0239	-0.3294	0.2799	0.1358	0.1167	-0.1058	-0.1443	-0.1435	-0.1244	0.2683	0.1029	0.0031	0.3991	-0.0281	0.1912	-47.6799	-24.6835	78.1269
11	2.2129	0.0377	-0.5121	0.6479	0.22	0.5005	-0.1563	-0.4464	0.3357	0.0551	0.1075	-0.0272	-0.1448	0.012	0.0538	0.3445	0.1092	-0.016	0.3411	-0.0799	0.2665	-53.9683	-21.2614	79.754
12	1.2146	-0.0346	-0.2946	0.7442	0.0596	1.1158	0.118	0.1741	0.0535	-0.1956	-0.1394	0.1021	-0.1166	-0.062	0.0042	0.2587	0.1191	-0.0458	0.2648	-0.1084	0.3332	-71.7228	-21.8868	-16.5913
13	0.3676	0.1302	-0.3979	1.0775	-0.2523	0.9916	-0.0243	0.069	-0.2565	-0.0008	-0.0995	0.2942	0.0887	-0.2049	0.0973	0.2147	0.0454	-0.0533	0.3077	-0.1612	0.5206	-84.5433	-36.5509	-5.0391
14	1.9254	-0.9401	-1.0256	1.7783	0.6869	1.1104	0.0676	0.4193	-0.1488	-0.1856	-0.1117	0.0572	0.0275	-0.1185	0.0436	0.2932	0.1025	-0.1435	0.5267	-0.2685	0.491	-83.4484	-35.0634	-26.75
15	0.7941	0.2152	-0.3769	0.348	-0.3058	0.3258	-0.0876	0.4185	-0.2263	-0.4022	-0.1265	0.2216	0.03	-0.3378	0.0468	0.3855	0.1332	-0.1175	0.5287	-0.253	0.4571	-78.0995	-33.4198	-31.4587
16	1.0214	0.0307	0.1366	0.8772	0.0972	0.9469	0.0049	-0.0196	-0.1297	0.0875	-0.0991	0.0257	-0.07	0.0274	0.0982	0.3442	0.0343	-0.0178	0.1851	0.0002	0.2543	-68.0365	1.9293	18.8914
17	0.4788	-0.3705	0.3344	1.7987	-0.2629	0.7946	-0.1677	-0.0845	0.029	-0.0528	0.0853	0.2866	-0.0262	-0.3513	0.0682	0.3984	0.076	-0.0116	0.2473	-0.0666	0.3803	-86.5327	12.6733	15.2488
18	0.531	-0.0477	-0.1565	1.0527	0.4458	0.2695	-0.0734	0.0006	0.0669	-0.1096	-0.0742	0.3621	-0.1655	-0.0024	0.1566	0.4235	0.0969	-0.0635	0.2626	-0.0678	0.3626	-83.4043	16.516	9.7159
19	1.537	-0.0352	0.14	0.8448	-0.0782	0.8625	-0.1446	-0.3711	0.0973	0.3491	-0.0444	0.1506	-0.1767	-0.0857	0.2042	0.4436	0.0505	0.031	0.2615	-0.0582	0.243	-75.9611	14.2916	33.3845
20	1.7139	0.7045	0.3202	1.2975	-0.2475	0.9891	0.338	-0.4588	-0.2062	0.1316	-0.1975	0.1359	0.1944	-0.1257	-0.1033	0.2973	-0.1329	-0.045	0.3271	0.0187	0.3003	-59.8717	-71.7484	28.5705
21	1.1724	0.5484	0.0476	1.3604	0.1501	0.096	0.2144	-0.2355	-0.0141	-0.1501	-0.0267	0.592	0.204	-0.2854	-0.0226	0.4257	-0.1239	-0.1896	0.3275	0.0359	0.5593	-77.9855	-75.2364	15.8661
22	1.1772	0.5398	-0.6122	1.7436	-0.6828	1.7892	0.2752	-0.1846	0.228	0.0006	-0.2908	0.3096	-0.2114	-0.2972	-0.2158	0.2048	-0.0651	0.0123	0.3841	-0.0703	0.5694	-75.5585	-57.53	24.9159
23	0.4173	-0.0195	0.0248	0.2801	-0.1727	0.4855	0.1516	-0.2306	0.3098	0.007	-0.1634	0.5483	-0.1007	-0.3314	-0.0432	0.2418	-0.0626	0.0751	0.4314	-0.1425	0.4973	-69.8891	-53.7611	27.4057

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 210 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 211 through 355 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 356 through 461 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 1 through 210 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 211 through 341 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 342 through 385 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 386 through 461 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 1 through 247 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 248 through 341 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 342 through 385 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 386 through 461 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 1 through 233 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 234 through 341 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 342 through 385 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 386 through 461 )
16	X-RAY DIFFRACTION	16	chain 'E' and (resid 1 through 210 )
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 211 through 247 )
18	X-RAY DIFFRACTION	18	chain 'E' and (resid 248 through 341 )
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 342 through 461 )
20	X-RAY DIFFRACTION	20	chain 'F' and (resid 1 through 209 )
21	X-RAY DIFFRACTION	21	chain 'F' and (resid 210 through 341 )
22	X-RAY DIFFRACTION	22	chain 'F' and (resid 342 through 385 )
23	X-RAY DIFFRACTION	23	chain 'F' and (resid 386 through 461 )

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Yorodumi