PDB-5naq: Crystal structure of native 6-phospho-glucosidase LpBgl from Lact...

ID or keywords:

Entry

Database: PDB / ID: 5naq

Title

Crystal structure of native 6-phospho-glucosidase LpBgl from Lactobacillus plantarum

Components

Beta-galactosidase

Keywords

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

Function / homology

Function and homology information

scopolin beta-glucosidase activity / beta-glucosidase / beta-glucosidase activity / carbohydrate metabolic process
Similarity search - Function

Biological species

Lactobacillus plantarum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.48 Å

Authors

Acebron, I. / Mancheno, J.M.

Funding support

Spain, 1items

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 1.2	Jan 17, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5naq.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb5naq.ent.gz	935.4 KB	Display	PDB format
PDBx/mmJSON format	5naq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5naq_validation.pdf.gz	499.2 KB	Display	wwPDB validaton report
Full document	5naq_full_validation.pdf.gz	528.9 KB	Display
Data in XML	5naq_validation.xml.gz	110.8 KB	Display
Data in CIF	5naq_validation.cif.gz	158.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/na/5naq ftp://data.pdbj.org/pub/pdb/validation_reports/na/5naq	HTTPS FTP

-
Related structure data

Related structure data	5navC 3cmjS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4xnz-d 2x6t-d 4ueq-d 6qwv-d 5ogk-d 1ha7-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

-
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

hetero molecules

329 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 on Superdex 200 10/300 reveals a large oligomer (apparently a hexamer).

Unit cell

Length a, b, c (Å)	196.688, 191.683, 105.931
Angle α, β, γ (deg.)	90.00, 102.75, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	C-649- HOH

#1: Protein	Beta-galactosidase Mass: 54666.910 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) / References: UniProt: F9ULH8, beta-glucosidase
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: PO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1605 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.97 Å³/Da / Density % sol: 58.65 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 15% (w/v) PEG 3350, 0.2 M di-ammonium phosphate, 0.1 M sodium cacodylate, pH 6.4, 2 mM DTT and detergent CTAB.

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.9794 Å
Detector	Type: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 28, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 2.48→61.233 Å / Num. obs: 126809 / % possible obs: 94 % / Redundancy: 3 % / B_iso Wilson estimate: 22.3 Å² / CC_1/2: 0.987 / R_merge(I) obs: 0.117 / R_pim(I) all: 0.076 / R_sym value: 0.14 / Net I/σ(I): 6.9
Reflection shell	Resolution: 2.48→2.61 Å / Redundancy: 2.9 % / R_merge(I) obs: 0.431 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 18978 / CC_1/2: 0.823 / R_pim(I) all: 0.281 / R_sym value: 0.517 / % possible all: 96.5

-
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: 3CMJ

3cmj

Resolution: 2.48→61.233 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.41

	R_factor	Num. reflection	% reflection
R_free	0.2168	6369	5.02 %
R_work	0.1588	-	-
obs	0.1618	126790	93.89 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å

Refinement step

Cycle: LAST / Resolution: 2.48→61.233 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	22392	0	60	1605	24057

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	23166
X-RAY DIFFRACTION	f_angle_d	0.993	31578
X-RAY DIFFRACTION	f_dihedral_angle_d	15.298	13278
X-RAY DIFFRACTION	f_chiral_restr	0.057	3210
X-RAY DIFFRACTION	f_plane_restr	0.006	4128

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 (%)
2.48-2.5082	0.2701	212	0.2157	4116	X-RAY DIFFRACTION	96
2.5082-2.5377	0.2862	208	0.1949	4169	X-RAY DIFFRACTION	97
2.5377-2.5686	0.2703	208	0.1877	4078	X-RAY DIFFRACTION	96
2.5686-2.6012	0.2867	223	0.191	4092	X-RAY DIFFRACTION	96
2.6012-2.6354	0.2845	240	0.1984	4067	X-RAY DIFFRACTION	96
2.6354-2.6715	0.275	207	0.196	4117	X-RAY DIFFRACTION	96
2.6715-2.7097	0.2778	196	0.1874	4100	X-RAY DIFFRACTION	96
2.7097-2.7501	0.2441	206	0.1826	4102	X-RAY DIFFRACTION	96
2.7501-2.7931	0.2469	199	0.1849	4084	X-RAY DIFFRACTION	95
2.7931-2.8389	0.2847	220	0.192	4054	X-RAY DIFFRACTION	95
2.8389-2.8878	0.2553	200	0.1976	4057	X-RAY DIFFRACTION	95
2.8878-2.9403	0.3067	209	0.1926	4075	X-RAY DIFFRACTION	95
2.9403-2.9969	0.272	185	0.1865	4097	X-RAY DIFFRACTION	95
2.9969-3.058	0.2435	216	0.1839	4038	X-RAY DIFFRACTION	95
3.058-3.1245	0.2772	202	0.1843	4058	X-RAY DIFFRACTION	95
3.1245-3.1972	0.2676	221	0.1866	4030	X-RAY DIFFRACTION	94
3.1972-3.2772	0.2374	208	0.1806	3971	X-RAY DIFFRACTION	94
3.2772-3.3658	0.2405	219	0.178	3983	X-RAY DIFFRACTION	93
3.3658-3.4648	0.2403	233	0.1757	3974	X-RAY DIFFRACTION	94
3.4648-3.5766	0.2246	231	0.1609	3970	X-RAY DIFFRACTION	94
3.5766-3.7044	0.1949	217	0.1531	3989	X-RAY DIFFRACTION	93
3.7044-3.8527	0.1922	210	0.1473	3930	X-RAY DIFFRACTION	93
3.8527-4.028	0.1964	196	0.1412	3999	X-RAY DIFFRACTION	92
4.028-4.2404	0.1903	210	0.1293	3950	X-RAY DIFFRACTION	92
4.2404-4.506	0.1703	248	0.1131	3887	X-RAY DIFFRACTION	92
4.506-4.8537	0.1421	211	0.114	3966	X-RAY DIFFRACTION	92
4.8537-5.3419	0.1773	211	0.1197	3926	X-RAY DIFFRACTION	91
5.3419-6.1143	0.1723	197	0.1345	3903	X-RAY DIFFRACTION	91
6.1143-7.701	0.1673	221	0.1368	3863	X-RAY DIFFRACTION	90
7.701-61.2516	0.1419	205	0.1303	3776	X-RAY DIFFRACTION	87

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	0.0591	-0.0011	0.0259	0.0486	-0.0265	0.0621	0.036	-0.0986	0.0021	0.1158	-0.0382	0.0095	-0.0581	-0.1253	-0.2463	0.1913	-0.0305	0.0341	0.1855	-0.0045	0.0567	66.4469	2.763	26.8126
2	0.0302	0.0031	0.0095	0.0201	0.0035	0.0047	0.0689	-0.0061	-0.028	0.0248	-0.0617	-0.1019	0.0073	0.02	-0.0012	0.1865	-0.0289	0.0175	0.1778	0.0218	0.0896	83.6748	3.2183	22.2931
3	0.0092	-0.0013	-0.0026	0.0057	0.0043	0.0032	-0.0011	-0.0057	0.0311	0.0335	0.0087	-0.0535	-0.088	0.0065	0	0.1558	-0.049	0.0024	0.1363	-0.0052	0.1328	85.1373	12.2609	10.0084
4	0.0898	0.065	0.0149	0.101	-0.0257	0.0237	0.0082	0.0735	-0.0353	-0.0084	0.0887	-0.1055	-0.0438	-0.1	0.022	0.1919	-0.026	0.0259	0.1548	-0.0009	0.1075	79.787	4.4168	8.4183
5	0.0426	0.0007	-0.0304	0.0181	-0.0386	0.0609	-0.0096	-0.0206	-0.2056	0.0564	0.0042	-0.0501	0.1311	0.0034	0	0.1586	-0.0255	0.0175	0.1365	0.0057	0.1971	77.9868	-13.7579	22.4869
6	0.2953	0.0212	-0.0171	0.1672	0.1369	0.2392	-0.0101	0.1895	0.1159	-0.1174	-0.099	0.0779	-0.1357	-0.1082	-0.0691	0.1538	0.0521	0.0384	0.1516	0.0178	0.1164	35.8501	16.6508	63.4372
7	0.052	-0.0097	-0.0166	0.0089	0.0063	0.0221	-0.0065	0.0123	0.0069	-0.032	-0.0092	-0.0612	-0.0275	0.0183	0.0137	0.1426	0.0504	0.0959	0.174	0.0155	0.0307	54.8157	5.706	68.0191
8	0.0756	-0.0416	0.0363	0.0418	0.0003	0.0487	-0.0548	-0.112	0.1317	0.0156	0.0109	-0.0212	-0.1263	-0.0255	-0.0052	0.1796	0.0181	0.0391	0.1681	-0.025	0.1536	46.1151	24.1013	79.6101
9	0.0937	0.0083	-0.0707	0.1212	0.0048	0.0588	0.0524	0.0389	0.0445	-0.0789	-0.0863	0.0817	-0.0132	0.0076	-0.0433	0.108	0.0554	-0.0059	0.1456	-0.0488	0.2077	5.0963	25.2731	86.8131
10	0.0689	0.02	-0.0102	0.0113	0.018	0.0969	-0.008	0.0282	-0.0562	-0.0192	-0.0185	0.0674	0.0094	-0.1016	-0.0323	0.0755	0.0204	-0.0388	0.172	-0.0714	0.3099	-12.5561	14.5568	92.8374
11	0.0139	-0.01	0.0428	0.0664	-0.0126	0.2516	0.056	0.0059	-0.1607	0.009	-0.0199	0.2091	0.0809	-0.0815	0.1103	0.1002	0.0094	-0.0073	0.1049	-0.097	0.3426	-8.6912	10.8418	97.9722
12	0.0205	-0.0141	0.0194	0.0192	-0.0175	0.0187	0.0373	0.0629	0.0059	-0.1224	-0.0123	0.1032	0.0506	0.0033	-0.0001	0.2048	0.0334	-0.0608	0.2575	-0.1521	0.3374	-7.8952	11.5968	76.7442
13	0.0106	0.0356	-0.0368	0.1172	-0.1282	0.1459	-0.0052	0.1603	-0.0823	-0.1822	-0.0419	0.1233	0.0571	-0.0015	-0.1568	0.1729	0.0576	-0.1032	0.2791	-0.1632	0.3023	-2.5717	13.2531	72.0939
14	0.1186	-0.0135	0.0129	0.1113	0.0798	0.0537	-0.024	-0.0148	-0.1337	0.0726	-0.0164	-0.0001	-0.0204	0.0148	-0	0.185	0.0126	0.0139	0.1654	0.0163	0.1739	6.8744	48.4333	122.3116
15	0.0328	0.0154	-0.0031	0.0084	0.005	0.0224	-0.0366	-0.0635	-0.0043	0.0061	-0.0668	0.0411	-0.0188	-0.0613	-0	0.2139	0.0609	0.0191	0.1811	0.021	0.2319	-10.318	53.4018	123.3298
16	0.0797	0.0002	0.0468	0.0358	-0.012	0.0242	-0.0701	-0.0298	0.0213	0.0182	-0.0536	0.1882	-0.0834	-0.0236	-0.0005	0.1911	0.0275	-0.027	0.1377	-0.0432	0.2129	-9.4244	63.2931	113.4471
17	0.0603	-0.0232	0.0225	0.1023	-0.0136	0.0078	-0.035	-0.0549	-0.0587	0.119	0.0255	0.1632	-0.107	0.0054	0.0164	0.2292	-0.0145	0.0762	0.2479	-0.0661	0.2006	-4.8053	61.5757	134.4203
18	0.0235	-0.0652	0.0474	0.1931	-0.1322	0.0956	-0.0589	-0.1876	0.0498	0.2298	-0.019	0.0263	-0.0936	-0.0523	-0.0529	0.2795	0.0059	0.0602	0.2914	-0.0421	0.1209	1.144	59.9744	138.2368
19	0.2081	0.0027	0.205	0.0034	-0.0052	0.209	-0.013	-0.1815	-0.0167	0.0422	0.027	-0.0249	0.0295	-0.1562	0.018	0.1966	0.0071	-0.0731	0.1583	-0.001	0.2043	38.4854	53.898	140.6039
20	0.1428	-0.0048	0.0515	0.0063	0.0006	0.071	-0.0674	0.0211	0.1057	-0.0277	-0.0269	-0.0526	-0.0583	0.1214	-0.1204	0.2514	-0.0064	-0.1578	0.1601	0.0425	0.2649	55.851	67.6976	136.3598
21	0.0456	0.0457	0.0138	0.0556	-0.0001	0.045	-0.0528	0.0733	-0.0248	-0.0201	-0.013	-0.0557	0.0459	0.0134	-0.0002	0.2006	0.0222	-0.0698	0.1551	-0.0146	0.2482	48.3393	49.6905	123.4794
22	0.5631	0.0333	0.1582	0.0987	-0.0434	0.1682	0.2599	-0.2781	-0.2121	0.171	-0.1062	0.0297	0.0403	-0.0276	0.3399	0.2318	-0.1587	0.0437	0.2305	0.0205	0.1238	38.2969	-24.9111	28.8837
23	0.0822	-0.079	-0.0607	0.1538	0.0743	0.0883	0.0838	-0.1238	-0.069	0.0472	-0.0922	0.2885	0.0312	-0.0727	-0.0118	0.2523	-0.1417	-0.0363	0.2324	0.0376	0.3456	20.228	-28.2798	16.1265
24	0.0343	-0.02	-0.0042	0.0091	0.0071	0.0101	0.0384	-0.1297	0.08	0.0693	-0.0643	0.1973	-0.0068	-0.0823	-0.1509	0.0482	-0.0869	0.2245	0.2502	-0.1366	0.2451	26.2764	-8.3259	26.9612

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 233 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 234 through 270 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 271 through 341 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 342 through 461 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 1 through 210 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 211 through 341 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 342 through 461 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 1 through 210 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 211 through 247 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 248 through 341 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 342 through 385 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 386 through 461 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 1 through 210 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 211 through 233 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 234 through 341 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 342 through 385 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 386 through 461 )
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 1 through 165 )
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 166 through 341 )
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 342 through 461 )
22	X-RAY DIFFRACTION	22	chain 'F' and (resid 1 through 210 )
23	X-RAY DIFFRACTION	23	chain 'F' and (resid 211 through 341 )
24	X-RAY DIFFRACTION	24	chain 'F' and (resid 342 through 461 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

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

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi