PDB-6efu: Crystal structure of the double mutant L167W / P172L of the beta-...

ID or keywords:

Entry

Database: PDB / ID: 6efu

Title

Crystal structure of the double mutant L167W / P172L of the beta-glucosidase from Trichoderma harzianum

Components

Beta-glucosidase

Keywords

HYDROLASE / GH1

Function / homology

Function and homology information

scopolin beta-glucosidase activity /

beta-glucosidase activity /

beta-glucosidase / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function

Biological species

Trichoderma harzianum (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.2 Å

Authors

Morais, M.A.B. / Santos, C.A. / Tonoli, C.C.C. / Souza, A.P. / Murakami, M.T.

Funding support

Brazil, 2items

Citation

Journal: Sci Rep / Year: 2019
Title: An engineered GH1 beta-glucosidase displays enhanced glucose tolerance and increased sugar release from lignocellulosic materials.
Authors: Santos, C.A. / Morais, M.A.B. / Terrett, O.M. / Lyczakowski, J.J. / Zanphorlin, L.M. / Ferreira-Filho, J.A. / Tonoli, C.C.C. / Murakami, M.T. / Dupree, P. / Souza, A.P.

History

Deposition	Aug 17, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 26, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jan 1, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Oct 11, 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	6efu.cif.gz	390.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6efu.ent.gz	321.2 KB	Display	PDB format
PDBx/mmJSON format	6efu.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ef/6efu ftp://data.pdbj.org/pub/pdb/validation_reports/ef/6efu	HTTPS FTP

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Related structure data

Related structure data	5bwfS S: Starting model for refinement
Similar structure data	1z4w-d 3ahy-2 3ahy-3 1z4x-d 1uyq-d 1z4y-d 1h49-1 1z50-d 7d6a-1 3ahy-4 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: Beta-glucosidase

B: Beta-glucosidase

hetero molecules

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

1

A: Beta-glucosidase

hetero molecules

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

2

B: Beta-glucosidase

hetero molecules

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

Unit cell

Length a, b, c (Å)	91.612, 96.213, 96.445
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Beta-glucosidase / Mass: 53249.410 Da / Num. of mol.: 2 / Mutation: L167W, P172L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trichoderma harzianum (fungus) / Gene: bgl, CI102_8745 / Production host: Escherichia coli (E. coli) References: UniProt: A0A127SA86, UniProt: A0A2T4AR08*PLUS, beta-glucosidase
#2: Chemical	ChemComp-NO3 / NITRATE ION / Nitrate Mass: 62.005 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: NO₃
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 290 / 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 Å³/Da / Density % sol: 38.51 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion / pH: 6.5 Details: PEG 3350 (20% w/v); 0.2 M sodium nitrate; 0.1 M Bis-tris propane pH 6.5

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

LNLS

/ Beamline: W01B-MX2 / Wavelength: 1.459 Å

Detector

Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 12, 2017

Radiation

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

Radiation wavelength

Wavelength: 1.459 Å / Relative weight: 1

Reflection

Resolution: 2.2→48.222 Å / Num. obs: 43877 / % possible obs: 99.9 % / Redundancy: 5.784 % / B_iso Wilson estimate: 36.97 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.149 / R_rim(I) all: 0.164 / Χ²: 0.921 / Net I/σ(I): 9.74

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2.2-2.33	5.774	1.382	1.27	6977	0.49	1.52	99.7
2.33-2.49	5.443	0.93	1.84	6570	0.654	1.03	99.9
2.49-2.69	6.066	0.675	2.78	6173	0.803	0.74	100
2.69-2.95	6.01	0.39	4.72	5667	0.92	0.427	100
2.95-3.3	5.654	0.204	8.5	5140	0.975	0.225	99.9
3.3-3.8	5.778	0.098	16.02	4576	0.994	0.108	100
3.8-4.65	6.065	0.059	24.94	3891	0.998	0.065	100
4.65-6.55	5.485	0.054	26.02	3087	0.998	0.06	99.9
6.55-48.222	5.674	0.035	37.89	1796	0.999	0.038	98.7

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing
PHENIX	(phenix.refine: 1.8.3_1479)	refinement
PDB_EXTRACT	3.24	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5BWF

5bwf

Resolution: 2.2→48.222 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.21

	R_factor	Num. reflection	% reflection
R_free	0.2211	2234	5.09 %
R_work	0.1784	-	-
obs	0.1806	43852	99.82 %

Solvent computation

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

Displacement parameters

B_iso max: 126.14 Å² / B_iso mean: 44.75 Å² / B_iso min: 21.78 Å²

Refinement step

Cycle: final / Resolution: 2.2→48.222 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7508	0	20	290	7818
B_iso mean	-	-	59	38.78	-
Num. residues	-	-	-	-	929

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	7750
X-RAY DIFFRACTION	f_angle_d	0.788	10528
X-RAY DIFFRACTION	f_chiral_restr	0.03	1071
X-RAY DIFFRACTION	f_plane_restr	0.004	1381
X-RAY DIFFRACTION	f_dihedral_angle_d	12.138	2787

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 16

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.2005-2.2483	0.3737	170	0.3026	2543	2713	99
2.2483-2.3006	0.3746	132	0.2839	2574	2706	100
2.3006-2.3581	0.2881	175	0.2766	2507	2682	100
2.3581-2.4219	0.3335	130	0.2677	2581	2711	100
2.4219-2.4932	0.3393	138	0.2502	2564	2702	100
2.4932-2.5736	0.2722	143	0.2395	2570	2713	100
2.5736-2.6656	0.3	91	0.2292	2639	2730	100
2.6656-2.7723	0.2583	125	0.2174	2607	2732	100
2.7723-2.8985	0.2545	126	0.2079	2579	2705	100
2.8985-3.0513	0.3038	118	0.2058	2606	2724	100
3.0513-3.2424	0.2383	157	0.1899	2604	2761	100
3.2424-3.4927	0.2221	134	0.1662	2614	2748	100
3.4927-3.844	0.1624	151	0.139	2590	2741	100
3.844-4.3999	0.154	142	0.1233	2652	2794	100
4.3999-5.5422	0.1586	124	0.1295	2668	2792	100
5.5422-48.2341	0.1936	178	0.1544	2720	2898	98

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	2.1616	-0.9702	1.3783	8.7969	-1.2261	0.9261	-0.8059	0.0119	-1.3917	0.0209	0.0717	-0.0405	1.7624	-0.6319	0.7019	0.5312	-0.1096	0.0737	0.5901	-0.0849	0.6733	79.037	-5.618	127.387
2	1.1715	-0.7482	-0.8658	1.2896	0.7331	2.9371	-0.3028	0.3965	-0.5813	0.0193	-0.2229	0.467	0.2798	-0.795	0.4818	0.3418	-0.1005	0.1108	0.5562	-0.2473	0.6378	58.703	7.178	142.035
3	1.8248	0.6204	0.7518	3.9412	1.1791	3.3521	-0.2979	-0.0328	-0.4989	0.2543	-0.0832	0.216	0.3797	-0.1921	0.3613	0.3146	-0.0338	0.1558	0.3508	-0.0698	0.4013	67.721	9.014	153.36
4	2.364	-0.4197	-0.4607	1.5729	0.9697	3.4829	-0.2054	0.1329	-0.3347	0.1031	0.0421	0.0345	-0.0136	0.2128	0.1418	0.2561	-0.0386	0.0787	0.3057	-0.0589	0.3091	74.642	14.498	149.547
5	4.9412	3.8666	-3.0154	5.1312	-1.8016	4.7686	-0.7275	-0.8817	-1.1035	-1.9816	-0.8541	-1.8318	1.8089	0.2564	1.5551	0.7789	0.1323	0.286	0.5647	-0.0074	0.8965	76.172	-8.52	146.963
6	0.8441	-0.0401	-2.3844	1.8291	-1.4201	3.9503	0.0768	-0.2851	0.0855	0.2497	-0.1389	-0.032	-0.3474	0.5159	0.0709	0.2705	-0.0507	-0.0071	0.4339	-0.0673	0.3462	86.831	17.861	143.553
7	2.4252	0.539	-1.1249	3.345	-0.32	3.4375	0.1389	-0.0931	0.3015	-0.0739	-0.1667	0.2674	-0.3473	-0.2102	0.0322	0.2647	0.0235	0.0592	0.4426	-0.1401	0.3806	82.754	20.812	131.127
8	8.5821	4.6983	3.0129	7.9217	-1.2126	9.2986	-0.638	1.0263	0.7144	-0.8044	0.2226	1.4824	-0.9192	-1.0253	0.3792	0.4835	0.1576	-0.1134	0.8802	-0.2402	0.6492	61.487	18.54	121.031
9	0.0295	-0.2163	-0.2151	1.4853	1.5973	1.7136	0.1516	0.9507	0.2864	-1.1331	-0.6578	1.3452	-0.7672	-1.1937	0.4796	0.5275	0.2674	-0.1163	0.9914	-0.3372	0.9408	62.784	14.643	116.367
10	2.8581	-1.0439	-0.4746	1.4478	0.8363	2.9954	0.0663	0.306	-0.1219	-0.1091	-0.392	0.4668	-0.0617	-0.9304	0.2905	0.3446	-0.0702	0.0373	0.66	-0.2222	0.4905	68.231	8.483	125.582
11	2.9589	-0.288	-0.4036	1.6195	0.7761	2.0679	0.1967	0.3463	0.1283	-0.5337	-0.1139	-0.0779	-0.2746	0.0135	-0.0815	0.451	0.0313	0.0352	0.2614	0.003	0.2011	113.407	13.96	97.585
12	6.5011	-1.313	0.7253	3.4486	0.3526	2.612	-0.0293	0.6711	0.3474	-0.5688	0.0352	-0.1523	-0.8829	0.1094	0.0471	0.6672	0.022	0.0831	0.3169	0.0553	0.3473	116.554	25.485	95.291
13	1.6424	-0.8164	-0.1604	4.095	-0.995	2.466	0.029	-0.0766	0.1682	-0.1599	0.0486	-0.313	-0.2218	0.251	-0.0783	0.227	-0.0367	0.0418	0.2546	-0.0444	0.2459	122.134	16.406	111.308
14	5.4437	6.137	-3.9924	9.3272	-4.8409	4.2236	0.0636	-0.0993	-0.0128	0.2928	0.0636	0.1765	-0.1383	-0.0505	-0.138	0.2325	0.0705	0.0439	0.2754	-0.0104	0.2316	104.133	9.077	123.731
15	3.4797	-0.8265	-0.8938	9.7127	-0.9684	3.054	-0.0517	-0.2475	-0.1413	0.4184	-0.0488	-0.4102	-0.0158	0.2319	0.1059	0.2676	0.0306	0.0092	0.3312	0.0168	0.2333	116.58	10.858	127.365
16	1.9585	0.8585	0.6488	2.6818	0.458	1.0645	-0.0201	-0.2091	-0.1554	0.1254	0.0137	-0.0693	0.1272	0.0228	0.0074	0.3087	0.0566	0.0598	0.3015	-0.032	0.2411	111.399	8.031	122.903
17	8.9669	-3.5816	5.2532	5.5102	-4.6925	4.7514	0.3781	0.7483	-0.4226	-0.294	0.3528	0.8013	0.4332	0.5524	-0.7197	0.4852	-0.1174	0.0465	0.392	-0.0636	0.5348	93.368	-5.108	119.263
18	2.8054	0.3419	0.5297	2.8029	0.0119	5.9487	0.0426	0.1557	-0.122	-0.1506	-0.0521	0.2729	0.5062	0.0661	-0.0375	0.2131	0.0465	-0.0002	0.269	0.0105	0.2419	100.013	9.334	113.11
19	7.9364	1.5459	-3.5373	7.2086	5.4574	9.4261	0.7088	0.2707	-0.9062	-0.6592	-0.7449	0.6292	0.7423	-0.8456	0.0878	0.6036	0.1069	-0.1293	0.4375	-0.0498	0.5329	92.409	3.1	95.56
20	3.0815	-1.603	-1.7784	2.8305	2.8481	5.2223	0.0231	0.3978	-0.1697	-0.3771	-0.1857	0.2435	-0.2783	-0.3969	0.1577	0.3376	0.0181	-0.0397	0.3038	0.0038	0.2845	98.09	12.159	101.881

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 1:7 )	A	1 - 7
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 8:113 )	A	8 - 113
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 114:158 )	A	114 - 158
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 159:212 )	A	159 - 212
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 213:218 )	A	213 - 218
6	X-RAY DIFFRACTION	6	( CHAIN A AND RESID 219:294 )	A	219 - 294
7	X-RAY DIFFRACTION	7	( CHAIN A AND RESID 295:366 )	A	295 - 366
8	X-RAY DIFFRACTION	8	( CHAIN A AND RESID 367:380 )	A	367 - 380
9	X-RAY DIFFRACTION	9	( CHAIN A AND RESID 381:387 )	A	381 - 387
10	X-RAY DIFFRACTION	10	( CHAIN A AND RESID 388:464 )	A	388 - 464
11	X-RAY DIFFRACTION	11	( CHAIN B AND RESID 1:87 )	B	1 - 87
12	X-RAY DIFFRACTION	12	( CHAIN B AND RESID 88:114 )	B	88 - 114
13	X-RAY DIFFRACTION	13	( CHAIN B AND RESID 115:213 )	B	115 - 213
14	X-RAY DIFFRACTION	14	( CHAIN B AND RESID 214:247 )	B	214 - 247
15	X-RAY DIFFRACTION	15	( CHAIN B AND RESID 248:276 )	B	248 - 276
16	X-RAY DIFFRACTION	16	( CHAIN B AND RESID 277:321 )	B	277 - 321
17	X-RAY DIFFRACTION	17	( CHAIN B AND RESID 322:333 )	B	322 - 333
18	X-RAY DIFFRACTION	18	( CHAIN B AND RESID 334:378 )	B	334 - 378
19	X-RAY DIFFRACTION	19	( CHAIN B AND RESID 379:389 )	B	379 - 389
20	X-RAY DIFFRACTION	20	( CHAIN B AND RESID 390:464 )	B	390 - 464

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