PDB-5jbo: Trichoderma harzianum GH1 beta-glucosidase ThBgl2

ID or keywords:

Entry

Database: PDB / ID: 5jbo

Title

Trichoderma harzianum GH1 beta-glucosidase ThBgl2

Components

Beta-glucosidase

Keywords

HYDROLASE / GH1 / beta-glucosidase / Trichoderma harzianum

Function / homology

Function and homology information

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

Biological species

Trichoderma harzianum (fungus)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.97 Å

Authors

Florindo, R.N. / Mutti, H.S. / Polikarpov, I. / Nascimento, A.S.

Funding support

Brazil, 4items

Organization	Grant number	Country
Sao Paulo Research Foundation (FAPESP)	2008/56255-9	Brazil
Sao Paulo Research Foundation (FAPESP)	2014/06565-2	Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)	485950/2013-8	Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)	490022/2009-0	Brazil

Citation

Journal: N Biotechnol / Year: 2018
Title: Structural insights into beta-glucosidase transglycosylation based on biochemical, structural and computational analysis of two GH1 enzymes from Trichoderma harzianum.
Authors: Florindo, R.N. / Souza, V.P. / Mutti, H.S. / Camilo, C. / Manzine, L.R. / Marana, S.R. / Polikarpov, I. / Nascimento, A.S.

History

Deposition	Apr 13, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 9, 2017	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 2017	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Dec 13, 2017	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.3	Mar 7, 2018	Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.4	Apr 17, 2019	Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5	Jan 1, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6	Sep 27, 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	5jbo.cif.gz	218.4 KB	Display	PDBx/mmCIF format
PDB format	pdb5jbo.ent.gz	171.8 KB	Display	PDB format
PDBx/mmJSON format	5jbo.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5jbo_validation.pdf.gz	406.1 KB	Display	wwPDB validaton report
Full document	5jbo_full_validation.pdf.gz	408.3 KB	Display
Data in XML	5jbo_validation.xml.gz	26.8 KB	Display
Data in CIF	5jbo_validation.cif.gz	43.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jb/5jbo ftp://data.pdbj.org/pub/pdb/validation_reports/jb/5jbo	HTTPS FTP

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Related structure data

Related structure data	5jbkC 3ahyS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5idi-1 1oif-2 5idi-2 2j7e-1 2j77-2 7d6a-1 2j78-1 6vch-3 2wc4-4 2wc4-1 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

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	57.519, 78.142, 100.272
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Beta-glucosidase Mass: 55311.836 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trichoderma harzianum (fungus) / Gene: THAR02_02251 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0F9XM91*PLUS
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 867 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	No match in UNP, the closest sequence in UNP is A0A0F9XM91, with 99.4% in sequence identity. Author ...No match in UNP, the closest sequence in UNP is A0A0F9XM91, with 99.4% in sequence identity. Author to deposit the sequence to UNP.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.04 Å³/Da / Density % sol: 39.8 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 MES pH 6.5, 25% PEG 8000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.54 Å
Detector	Type: APEX II CCD / Detector: CCD / Date: Jul 1, 2013
Radiation	Monochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 1.97→61.64 Å / Num. obs: 32663 / % possible obs: 100 % / Redundancy: 4.5 % / Net I/σ(I): 8.7

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Processing

Software

Name	Version	Classification
PHENIX	1.10.1-2155_1692	refinement
iMOSFLM		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3AHY

3ahy

Resolution: 1.97→61.64 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.65

	R_factor	Num. reflection	% reflection
R_free	0.2025	1655	5.07 %
R_work	0.1681	-	-
obs	0.1698	32653	99.96 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.97→61.64 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3797	0	0	867	4664

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	3913
X-RAY DIFFRACTION	f_angle_d	0.601	5321
X-RAY DIFFRACTION	f_dihedral_angle_d	10.514	2267
X-RAY DIFFRACTION	f_chiral_restr	0.041	535
X-RAY DIFFRACTION	f_plane_restr	0.004	700

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 (%)
1.97-2.028	0.271	125	0.2209	2533	X-RAY DIFFRACTION	100
2.028-2.0934	0.232	132	0.1999	2539	X-RAY DIFFRACTION	100
2.0934-2.1683	0.2594	145	0.1995	2546	X-RAY DIFFRACTION	100
2.1683-2.2551	0.2201	131	0.1864	2570	X-RAY DIFFRACTION	100
2.2551-2.3577	0.2235	157	0.1816	2526	X-RAY DIFFRACTION	100
2.3577-2.482	0.2221	132	0.1802	2563	X-RAY DIFFRACTION	100
2.482-2.6375	0.2156	146	0.1746	2573	X-RAY DIFFRACTION	100
2.6375-2.8412	0.209	140	0.1666	2553	X-RAY DIFFRACTION	100
2.8412-3.1271	0.1836	129	0.1587	2598	X-RAY DIFFRACTION	100
3.1271-3.5795	0.186	137	0.1441	2621	X-RAY DIFFRACTION	100
3.5795-4.5096	0.1425	156	0.1303	2604	X-RAY DIFFRACTION	100
4.5096-61.6662	0.193	125	0.1612	2772	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	3.7406	-0.4298	4.2857	7.8288	-2.4755	8.6824	0.1433	0.0143	-0.5116	-0.0913	-0.0334	-0.1628	0.4513	-0.0478	-0.16	0.2366	-0.0135	0.0682	0.1407	-0.0163	0.2003	19.0434	20.5521	13.4301
2	1.0034	0.0597	0.0776	0.5186	-0.1259	1.1829	-0.0231	-0.01	0.0747	0.108	-0.0102	-0.0137	-0.2031	0.0229	-0.013	0.0407	0.0108	-0.0014	0.0537	-0.0095	0.0495	38.1095	46.8646	15.1382
3	1.1839	0.4095	-0.3753	1.0905	-0.6565	1.4701	0.0202	0.1584	0.0968	-0.0575	0.1963	0.0356	-0.2835	-0.0669	-0.0033	0.1439	0.0061	0.0258	0.0663	0.0097	0.0911	34.8376	58.599	13.3601
4	1.798	0.2945	-0.665	0.9706	0.5539	1.0834	0.0212	-0.0372	0.1278	0.0825	0.0719	0.0401	-0.1374	0.0849	0.1924	0.0748	-0.0002	-0.0768	0.0764	0.0444	-0.0368	37.8297	46.1769	24.3627
5	0.5102	-0.0818	-0.0171	0.24	-0.0698	0.9893	0.0015	-0.0285	-0.03	0.0279	0.0026	-0.0511	-0.0121	0.0661	-0.0029	0.0491	0.0044	-0.0024	0.0366	-0.0021	0.0595	44.0364	37.7624	14.0741
6	0.8242	-0.0331	0.3375	1.0604	-0.289	1.189	-0.0228	0.0413	0.139	-0.0695	-0.0177	0.0657	-0.1367	0.0336	0.0041	0.0431	-0.0112	0.0102	0.0641	-0.0081	0.0536	38.4181	48.038	-3.3519
7	1.8194	1.0915	0.3933	3.7873	-0.7214	0.6253	0.0871	0.1758	-0.324	-0.1727	0.1326	-0.059	0.4092	0.1457	0.1049	0.1819	0.0105	-0.0159	0.0795	-0.0351	0.0813	49.1354	24.0258	4.5493
8	1.0597	-0.3388	0.0917	1.2056	-0.2618	0.5712	0.0069	0.2348	-0.4097	-0.1954	0.1397	0.12	0.6754	-0.0254	0.0431	0.31	-0.0156	-0.0128	0.0903	-0.0493	0.1089	46.5178	20.8503	9.9026
9	1.1089	-0.7063	0.7795	0.6079	-0.3918	1.0802	0.022	0.0125	-0.0362	-0.0319	-0.0059	0.0624	0.0112	-0.1209	-0.0267	0.0819	-0.0077	0.0043	0.0531	-0.0098	0.0469	21.2811	37.6385	-7.8497
10	1.047	-0.1838	-0.4084	1.2883	-0.1467	1.0385	0.0017	0.1385	-0.1116	-0.0888	-0.0308	-0.0646	0.1613	-0.0404	0.0562	0.0579	-0.0143	0.0151	0.0833	-0.0148	0.0356	34.0755	34.7539	-9.8475
11	1.1572	-0.4443	0.0361	1.4401	-0.2433	1.0233	-0.0463	-0.0138	-0.1334	-0.1961	0.0917	0.0074	0.1425	-0.0011	0.0134	0.065	0.0092	0.0123	0.0821	-0.0156	0.0573	41.8817	35.1858	-12.5843
12	0.2882	0.2441	-0.1327	0.5373	0.2793	0.9016	0.012	-0.0776	0.0372	0.0017	-0.0064	0.0551	0.0258	-0.1207	0.0355	0.0545	0.0011	0.0096	0.0252	0.016	0.0589	23.7341	37.1259	-0.5209
13	3.0235	0.412	0.2755	1.0069	0.9451	0.8863	-0.1638	0.3839	0.4758	-0.3621	0.3205	0.1036	-0.2215	-0.1948	0.2231	0.1518	-0.031	-0.0286	0.1361	0.0676	0.1377	25.9256	50.1216	-15.3596
14	6.1715	0.6129	-1.3359	1.8863	-0.0308	1.524	0.0489	-0.189	0.092	-0.0702	-0.1533	0.1505	-0.0731	-0.1778	0.0144	0.0994	0.0317	-0.0107	0.1249	-0.011	0.0711	12.8574	46.8399	-7.232
15	1.5838	0.3676	1.0428	1.4565	0.8178	3.0172	-0.0437	-0.1898	0.1346	0.0788	-0.071	0.0655	-0.0318	-0.2404	0.1526	0.0886	0.007	0.0137	0.0823	0.0176	0.1078	13.756	45.7683	4.9759
16	3.6497	0.3997	0.4077	4.5164	1.7383	6.2576	0.1097	0.3425	-0.0597	-0.1232	0.0258	0.7258	-0.0339	-0.5818	0.0134	0.0951	-0.0342	-0.0129	0.1287	0.0031	0.1289	14.5663	32.3256	1.4339
17	0.653	-0.0552	-0.0655	0.322	-0.1725	1.365	-0.0494	0.0109	-0.0162	-0.1269	0.0524	-0.0328	0.0917	-0.0649	0.0325	0.0523	-0.0202	0.0024	0.0445	-0.0103	0.0595	23.9672	33.1084	4.5753
18	1.0585	-0.5867	-0.3499	1.2826	0.5117	2.1508	0.0071	-0.011	-0.087	-0.0944	-0.1058	0.171	-0.1377	-0.2929	0.0258	0.0516	-0.0055	0.0029	0.096	0.0299	0.079	15.1224	37.5092	15.2344
19	0.7593	0.1921	-0.1901	0.739	-0.0537	0.9596	-0.015	-0.066	0.0322	0.0138	0.0524	0.0336	-0.1078	0.0067	-0.0076	0.0333	0.0118	-0.011	0.0774	0.0104	0.0518	25.3986	42.4652	18.5933
20	2.1773	-1.59	0.363	3.2338	0.4907	4.2483	0.0133	-0.0729	-0.3615	0.0131	0.0347	0.4611	0.2345	-0.2068	-0.0246	0.1222	-0.0216	0.0342	0.1786	0.0281	0.1953	16.948	25.8507	20.2156

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 6:11)
2	X-RAY DIFFRACTION	2	(chain A and resid 12:44)
3	X-RAY DIFFRACTION	3	(chain A and resid 45:55)
4	X-RAY DIFFRACTION	4	(chain A and resid 56:60)
5	X-RAY DIFFRACTION	5	(chain A and resid 61:171)
6	X-RAY DIFFRACTION	6	(chain A and resid 172:222)
7	X-RAY DIFFRACTION	7	(chain A and resid 223:227)
8	X-RAY DIFFRACTION	8	(chain A and resid 228:233)
9	X-RAY DIFFRACTION	9	(chain A and resid 234:264)
10	X-RAY DIFFRACTION	10	(chain A and resid 265:285)
11	X-RAY DIFFRACTION	11	(chain A and resid 286:307)
12	X-RAY DIFFRACTION	12	(chain A and resid 308:323)
13	X-RAY DIFFRACTION	13	(chain A and resid 324:336)
14	X-RAY DIFFRACTION	14	(chain A and resid 337:345)
15	X-RAY DIFFRACTION	15	(chain A and resid 346:361)
16	X-RAY DIFFRACTION	16	(chain A and resid 362:367)
17	X-RAY DIFFRACTION	17	(chain A and resid 368:392)
18	X-RAY DIFFRACTION	18	(chain A and resid 393:423)
19	X-RAY DIFFRACTION	19	(chain A and resid 424:470)
20	X-RAY DIFFRACTION	20	(chain A and resid 471:480)

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