PDB-6wgd: Crystal structure of a 6-phospho-beta-glucosidase from Bacillus l...

ID or keywords:

Entry

Database: PDB / ID: 6wgd

Title

Crystal structure of a 6-phospho-beta-glucosidase from Bacillus licheniformis

Components

6-phospho-beta-glucosidase

Keywords

HYDROLASE / 6-phospho-beta-glucosidase / GH1 / bacillus licheniformis

Function / homology

Function and homology information

6-phospho-beta-glucosidase / 6-phospho-beta-glucosidase activity / methyl beta-D-glucoside 6-phosphate glucohydrolase activity / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function

Biological species

Bacillus licheniformis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.2 Å

Authors

Liberato, M.V. / Popov, A. / Polikarpov, I.

Funding support

Brazil, 3items

Organization	Grant number	Country
Sao Paulo Research Foundation (FAPESP)	2015/13684-0	Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)	423693/2016-6	Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)	303988/2016-9	Brazil

Citation

Journal: J.Chem.Inf.Model. / Year: 2020
Title: X-ray Structure, Bioinformatics Analysis, and Substrate Specificity of a 6-Phospho-beta-glucosidase Glycoside Hydrolase 1 Enzyme from Bacillus licheniformis .
Authors: Veldman, W. / Liberato, M.V. / Almeida, V.M. / Souza, V.P. / Frutuoso, M.A. / Marana, S.R. / Moses, V. / Tastan Bishop, O. / Polikarpov, I.

History

Deposition	Apr 5, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 25, 2020	Provider: repository / Type: Initial release
Revision 1.1	Jan 13, 2021	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2	Oct 18, 2023	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

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Download

PDBx/mmCIF format	6wgd.cif.gz	541.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6wgd.ent.gz	447.1 KB	Display	PDB format
PDBx/mmJSON format	6wgd.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6wgd_validation.pdf.gz	453.9 KB	Display	wwPDB validaton report
Full document	6wgd_full_validation.pdf.gz	457.9 KB	Display
Data in XML	6wgd_validation.xml.gz	49.7 KB	Display
Data in CIF	6wgd_validation.cif.gz	70 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wg/6wgd ftp://data.pdbj.org/pub/pdb/validation_reports/wg/6wgd	HTTPS FTP

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Related structure data

Related structure data	4iplS S: Starting model for refinement
Similar structure data	3scw-2 4ptx-2 4qll-2 4gxp-1 3sct-2 6a7j-d 3scu-2 3sco-2 3vij-d 3sct-1 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

4iplS

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: 6-phospho-beta-glucosidase

B: 6-phospho-beta-glucosidase

C: 6-phospho-beta-glucosidase

hetero molecules

161 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: 6-phospho-beta-glucosidase

hetero molecules

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

2

B: 6-phospho-beta-glucosidase

hetero molecules

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

3

C: 6-phospho-beta-glucosidase

hetero molecules

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

Unit cell

Length a, b, c (Å)	98.272, 98.272, 285.734
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	152
Space group name H-M	P3₁21

#1: Protein	6-phospho-beta-glucosidase Mass: 53453.184 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus licheniformis (bacteria) / Gene: ascB, GII88_21755 / Production host: Escherichia coli (E. coli) References: UniProt: A0A5Q3BW14, UniProt: Q65D37*PLUS, 6-phospho-beta-glucosidase
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 449 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.48 Å³/Da / Density % sol: 50.48 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 15% PEG4000, 0.1 M ammonium sulphate, and 0.1 M Tris, pH 7.0

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID23-1 / Wavelength: 0.98 Å

Detector

Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 18, 2013

Radiation

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

Radiation wavelength

Wavelength: 0.98 Å / Relative weight: 1

Reflection

Resolution: 2.2→49.14 Å / Num. obs: 82240 / % possible obs: 99.9 % / Redundancy: 5.5 % / CC_1/2: 0.996 / R_merge(I) obs: 0.139 / R_pim(I) all: 0.065 / R_rim(I) all: 0.153 / Net I/σ(I): 7.7 / Num. measured all: 456034 / Scaling rejects: 9

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. measured all	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Net I/σ(I) obs	% possible all
2.2-2.24	5.7	1.54	25655	4485	0.86	0.704	1.696	1.5	99.8
11.43-49.14	4.7	0.067	3295	697	0.997	0.033	0.076	20.4	98.7

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	4.25 Å	48.43 Å
Translation	4.25 Å	48.43 Å

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Processing

Software

Name	Version	Classification
Aimless	0.7.4	data scaling
PHASER	2.8.3	phasing
PHENIX	1.17.1	refinement
PDB_EXTRACT	3.25	data extraction
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4IPL

4ipl

Resolution: 2.2→48.425 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.86

	R_factor	Num. reflection	% reflection
R_free	0.2441	4077	4.97 %
R_work	0.21	-	-
obs	0.2117	81976	99.66 %

Solvent computation

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

Displacement parameters

B_iso max: 103.65 Å² / B_iso mean: 51.1029 Å² / B_iso min: 23.25 Å²

Refinement step

Cycle: final / Resolution: 2.2→48.425 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10631	0	20	449	11100
B_iso mean	-	-	51.77	46.95	-
Num. residues	-	-	-	-	1358

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 (%)
2.2-2.2259	0.3393	117	0.3508	2636	99
2.2259-2.253	0.3961	134	0.3289	2670	99
2.253-2.2815	0.3909	168	0.3277	2636	100
2.2815-2.3116	0.3552	153	0.3091	2607	99
2.3116-2.3432	0.3606	152	0.307	2666	100
2.3432-2.3767	0.3426	148	0.299	2588	99
2.3767-2.4122	0.3253	156	0.2878	2630	99
2.4122-2.4499	0.3609	137	0.2886	2669	100
2.4499-2.49	0.3027	143	0.2857	2637	100
2.49-2.533	0.3375	134	0.276	2672	99
2.533-2.579	0.323	133	0.2737	2706	100
2.579-2.6286	0.2982	137	0.2565	2621	100
2.6286-2.6823	0.322	128	0.2506	2679	99
2.6823-2.7406	0.2817	122	0.2471	2673	100
2.7406-2.8043	0.2823	154	0.2404	2659	100
2.8043-2.8745	0.2796	151	0.2301	2651	100
2.8745-2.9522	0.3224	94	0.2266	2730	100
2.9522-3.039	0.2653	145	0.2299	2657	100
3.039-3.1371	0.2534	142	0.236	2680	100
3.1371-3.2492	0.3191	142	0.2323	2705	100
3.2492-3.3793	0.2467	126	0.2172	2687	100
3.3793-3.533	0.2296	134	0.2065	2705	100
3.533-3.7192	0.214	158	0.1916	2681	100
3.7192-3.9521	0.2052	152	0.1771	2719	100
3.9521-4.2571	0.19	142	0.1648	2745	100
4.2571-4.6852	0.1638	134	0.1461	2725	100
4.6852-5.3624	0.1787	140	0.1597	2754	100
5.3624-6.7532	0.2097	149	0.1876	2773	100
6.7532-48.425	0.2293	152	0.1796	2938	99

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	1.4705	0.3716	-0.1758	1.37	0.2001	1.4914	0.2009	0.1781	0.1725	-0.0474	-0.0631	0.0176	-0.2819	-0.0141	-0.1233	0.457	0.0623	0.1075	0.4963	0.0414	0.3522	4.9156	13.2441	16.3889
2	6.1644	-0.323	1.9853	1.3064	0.3045	3.967	-0.0019	-0.3187	-0.0144	0.1155	0.085	-0.0404	-0.5482	0.1109	-0.0879	0.4484	-0.0014	0.1242	0.4213	-0.0162	0.3447	10.341	14.5398	27.7536
3	1.1966	-0.2665	-0.5144	1.3877	0.1503	3.4788	0.1746	-0.1606	0.1124	0.1195	-0.0031	-0.0182	-0.1408	0.5455	-0.1758	0.4624	0.0196	0.111	0.6083	-0.0279	0.4039	7.7064	11.6427	40.3377
4	1.2426	-0.197	-0.8833	0.4792	0.9117	4.0028	0.0735	0.0076	-0.0919	0.1199	0.0357	0.0245	0.3605	-0.0127	-0.1117	0.3928	0.0358	0.0225	0.3982	0.0311	0.3319	-0.9374	-3.0645	23.8964
5	1.4497	-0.3705	-0.1448	0.982	-0.2666	1.1558	0.1405	-0.237	0.1493	0.4382	-0.1143	0.0852	-0.5622	0.1098	-0.0172	0.9104	-0.0689	0.0957	0.4864	-0.032	0.3121	43.9601	35.8039	57.1813
6	2.484	0.2397	0.0886	1.3507	-0.2899	2.4354	0.168	0.1118	0.2664	0.3453	-0.1296	0.2704	-0.6227	-0.1844	-0.0346	0.7734	0.0873	0.1528	0.3641	-0.0053	0.3773	37.6727	42.6311	43.8181
7	0.2537	-0.2077	0.2259	2.4673	1.6203	3.6669	-0.0354	0.0677	-0.0218	-0.0083	0.0689	0.0619	-0.4186	0.229	-0.0282	0.478	-0.0019	0.0679	0.4933	-0.0025	0.315	43.5928	28.8501	29.6322
8	0.8857	-0.236	0.4211	1.761	0.5665	1.6106	0.0383	0.1637	0.1031	0.0735	-0.1031	0.1725	-0.459	-0.1151	0.0573	0.4526	0.0624	0.0977	0.5475	0.0478	0.3245	38.8359	36.2372	29.3597
9	6.6451	1.1726	0.795	1.1943	-0.1422	2.1912	0.0771	-1.2253	-0.8827	0.2263	-0.1109	0.0933	0.6066	-0.6758	0.0855	0.6345	-0.0167	0.089	0.6672	0.0848	0.4856	37.9396	10.1623	35.1262
10	1.2254	0.321	-0.383	0.8819	-0.5418	3.1918	0.1534	-0.087	-0.0892	0.3058	-0.1451	-0.0107	0.0844	0.3943	-0.0021	0.5743	0.0056	-0.013	0.4321	-0.001	0.3093	52.7034	21.6702	48.9438
11	1.3567	-0.3428	0.0422	1.9464	-0.1975	2.6459	-0.032	-0.4337	0.0836	0.2133	0.0183	0.0986	-0.5256	-0.3424	0.0326	0.5465	0.086	-0.0058	0.7258	-0.0192	0.3021	46.6098	-18.0656	9.7179
12	3.823	-0.2927	0.4907	1.7916	-0.8899	4.1537	-0.1374	-0.1788	0.2601	-0.1126	0.1567	0.1405	-0.7613	-0.5363	-0.0074	0.6497	0.1288	-0.0033	0.4687	-0.0346	0.3092	44.9513	-10.3052	-3.4725
13	1.3726	1.9734	1.2892	4.5922	2.2637	3.2633	-0.0991	0.1229	0.0868	-0.0045	0.0392	0.1875	-0.1256	0.2351	0.0401	0.4783	0.0439	0.0223	0.4538	-0.0153	0.2987	43.822	-24.7284	-15.9028
14	1.2295	0.6827	0.3811	2.6155	0.463	1.7905	-0.0257	-0.0106	0.0526	0.1006	-0.0151	0.2374	-0.2882	-0.2205	0.0361	0.4298	0.1317	0.0212	0.5054	-0.021	0.284	39.6311	-23.7715	-13.7774
15	1.8279	0.3009	-0.3176	0.5445	-0.2337	4.1663	0.044	-0.4007	-0.2935	0.0919	-0.0297	-0.0161	0.4543	0.0832	0.0051	0.4545	0.099	-0.0172	0.4787	0.0483	0.3456	48.8938	-35.7071	2.933

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 162 )	A	4 - 162
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 163 through 196 )	A	163 - 196
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 197 through 289 )	A	197 - 289
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 290 through 469 )	A	290 - 469
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 5 through 119 )	B	5 - 119
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 120 through 222 )	B	120 - 222
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 223 through 266 )	B	223 - 266
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 267 through 315 )	B	267 - 315
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 316 through 346 )	B	316 - 346
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 347 through 469 )	B	347 - 469
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 4 through 145 )	C	4 - 145
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 146 through 222 )	C	146 - 222
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 223 through 266 )	C	223 - 266
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 267 through 345 )	C	267 - 345
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 346 through 469 )	C	346 - 469

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