PDB-4ptw: Halothermothrix orenii beta-glucosidase A, 2-deoxy-2-fluoro-gluco...

ID or keywords:

Entry

Database: PDB / ID: 4ptw

Title

Halothermothrix orenii beta-glucosidase A, 2-deoxy-2-fluoro-glucose complex

Components

Glycoside hydrolase family 1

Keywords

HYDROLASE / (beta/alpha)8 fold / TIM barrel / glycoside hydrolase / beta-glucosidase

Function / homology

Function and homology information

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

Biological species

Halothermothrix orenii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Hassan, N. / Nguyen, T.H. / Kori, L.D. / Patel, B.K.C. / Haltrich, D. / Divne, C. / Tan, T.C.

Citation

Journal: Appl.Microbiol.Biotechnol. / Year: 2015
Title: Biochemical and structural characterization of a thermostable beta-glucosidase from Halothermothrix orenii for galacto-oligosaccharide synthesis.
Authors: Hassan, N. / Nguyen, T.H. / Intanon, M. / Kori, L.D. / Patel, B.K. / Haltrich, D. / Divne, C. / Tan, T.C.

History

Deposition	Mar 11, 2014	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Sep 24, 2014	Provider: repository / Type: Initial release
Revision 1.1	Dec 11, 2019	Group: Data collection / Database references / Category: reflns_shell / struct_ref_seq_dif Item: _reflns_shell.pdbx_Rsym_value / _struct_ref_seq_dif.details
Revision 1.2	Jul 29, 2020	Group: Data collection / Derived calculations Category: chem_comp / pdbx_chem_comp_identifier ...chem_comp / pdbx_chem_comp_identifier / struct_site / struct_site_gen Item: _chem_comp.type / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3	Aug 24, 2022	Group: Database references / Structure summary Category: chem_comp / citation ...chem_comp / citation / citation_author / database_2 Item: _chem_comp.pdbx_synonyms / _citation.journal_volume ..._chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4	Nov 8, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4ptw.cif.gz	367.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4ptw.ent.gz	299.2 KB	Display	PDB format
PDBx/mmJSON format	4ptw.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pt/4ptw ftp://data.pdbj.org/pub/pdb/validation_reports/pt/4ptw	HTTPS FTP

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Related structure data

Related structure data	4ptvC 4ptxC 3ta9S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2wc4-1 2wc4-3 2ces-1 6ziv-4 2cbv-1 1w3j-1 1oif-1 4ptv-2 2j79-1 2o9p-d 2z1s-d 2j79-2 2j77-2 3ta9-1 2j78-2 2j7f-1 5idi-2 2cbu-2 2j78-1 4gxp-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

4ptvC

4ptxC

3ta9S

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Glycoside hydrolase family 1

B: Glycoside hydrolase family 1

hetero molecules

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

1

A: Glycoside hydrolase family 1

hetero molecules

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

2

B: Glycoside hydrolase family 1

hetero molecules

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

Unit cell

Length a, b, c (Å)	88.983, 97.540, 109.616
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein

Glycoside hydrolase family 1

Mass: 52285.539 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Halothermothrix orenii (bacteria) / Strain: H 168 / Gene: bgla, Hore_15280 / Plasmid: pNIC28-Bsa4 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B8CYA8, beta-glucosidase

#2: Sugar

ChemComp-G2F / 2-deoxy-2-fluoro-alpha-D-glucopyranose / 2-deoxy-2-fluoro-alpha-D-glucose / 2-deoxy-2-fluoro-D-glucose / 2-deoxy-2-fluoro-glucose

Type: D-saccharide, alpha linking / Mass: 182.147 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C₆H₁₁FO₅

#3: Chemical

ChemComp-PG4 / TETRAETHYLENE GLYCOL

Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM

#4: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 409 / 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: 2.27 Å³/Da / Density % sol: 45.92 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: sodium cacodylate, sodium acetate, PEG 3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93935 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 2, 2012 / Details: Toroidal focusing mirror
Radiation	Monochromator: channel cut ESRF monochromator, Si(111) crystal Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.93935 Å / Relative weight: 1
Reflection	Resolution: 2→47.781 Å / Num. all: 64629 / Num. obs: 64629 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / R_sym value: 0.157 / Net I/σ(I): 12.4
Reflection shell	Resolution: 2→2.1 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 8644 / R_sym value: 1.31 / % possible all: 98.8

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Processing

Software

Name	Version	Classification
MxCuBE		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.8.2_1309)	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3TA9

3ta9

Resolution: 2→47.78 Å / SU ML: 0.25 / σ(F): 1.35 / Phase error: 23.57 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2349	2000	3.09 %	random
R_work	0.1774	-	-	-
all	0.1792	64627	-	-
obs	0.1792	64627	99.29 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2→47.78 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7296	0	46	409	7751

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	7566
X-RAY DIFFRACTION	f_angle_d	1.065	10247
X-RAY DIFFRACTION	f_dihedral_angle_d	16.355	2793
X-RAY DIFFRACTION	f_chiral_restr	0.075	1030
X-RAY DIFFRACTION	f_plane_restr	0.004	1329

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
2-2.05	0.3109	139	0.264	4366	99
2.05-2.1055	0.345	142	0.2467	4407	99
2.1055-2.1674	0.3242	140	0.2304	4437	99
2.1674-2.2374	0.2815	141	0.2168	4389	99
2.2374-2.3173	0.3151	142	0.2191	4438	99
2.3173-2.4101	0.2833	141	0.1932	4419	99
2.4101-2.5198	0.2026	141	0.1833	4426	99
2.5198-2.6526	0.2643	142	0.1793	4448	99
2.6526-2.8188	0.2605	143	0.1831	4484	99
2.8188-3.0364	0.2489	144	0.1875	4483	100
3.0364-3.3419	0.2228	143	0.173	4492	100
3.3419-3.8253	0.2029	144	0.1536	4534	100
3.8253-4.8188	0.1623	147	0.1322	4567	100
4.8188-47.7951	0.2222	151	0.1675	4737	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	0.0163	0.0088	0.0046	0.0211	0.005	0.0096	0.0107	0.0095	0.0155	0.0058	0.0056	-0.0064	0.0035	0.0038	0.0147	0.0226	0.0279	-0.0219	0.0281	0.0081	0.084	6.8132	109.867	22.705
2	0.0061	0.0017	0.0078	0.0017	0.0003	0.0437	0.0213	-0.04	0.0429	0.0401	-0.0113	0.0104	0.0307	-0.0622	0.0026	0.0578	0.0124	0.0069	0.0546	-0.0102	0.0758	-0.8948	105.3926	28.9019
3	0.0101	-0.012	0.0258	0.0299	-0.0335	0.0651	0.0528	0.0209	-0.0222	-0.1065	-0.0102	0.005	0.0527	0.012	0.0208	0.0641	0.0259	0.0015	0.0433	-0.0041	0.0716	4.225	99.4813	12.7353
4	0.0282	-0.0127	0.0114	0.0618	0.0403	0.0451	0.03	0.0901	0.0061	-0.152	-0.0103	-0.0137	0.012	0.0379	0.032	0.1391	0.0495	0.0283	0.0167	-0.0518	-0.0792	5.1875	106.7447	-2.9272
5	0.0073	-0.007	-0.0108	0.0056	0.0069	0.0177	-0.0067	0.0257	0.0023	-0.0718	0.0218	-0.0669	-0.0417	0.025	0.0097	0.0916	0.0034	0.0661	0.0573	0.0139	0.0784	12.2075	118.2684	-0.837
6	0.0132	-0.0078	-0.0103	0.0135	-0.0104	0.0365	0.0481	0.0115	0.0106	-0.0626	-0.012	0.0075	-0.0338	0.0053	0.0612	0.1489	0.0017	-0.0482	0.0311	0.0248	0.043	1.8941	121.6054	4.3288
7	0.017	-0.0078	0.0037	0.0241	-0.0045	0.0012	0.0129	0.021	0.0293	-0.0058	0.0013	-0.0274	-0.0775	-0.014	0.0316	0.1787	0.0543	-0.0775	-0.0426	0.0171	0.0987	-0.1597	125.2927	17.6026
8	0.0083	0.0122	-0.0027	0.0198	-0.0022	0.002	0.0029	-0.0234	0.028	0.0415	-0.0034	-0.0025	-0.0452	-0.0055	-0.0005	0.1137	0.0508	-0.0651	0.0059	0.0063	0.0787	2.1586	123.3732	26.3278
9	0.0334	0.0047	0.0144	0.0075	-0.0176	0.0531	-0.0071	-0.0088	0.0109	-0.0128	0.0236	-0.0394	-0.0506	0.0255	0.015	0.0429	0.0547	-0.0037	0.0887	-0.0246	0.1003	41.6437	86.9014	-1.7029
10	0.0118	-0.0033	-0.0079	0.0145	-0.0032	0.0173	-0.0102	0.0113	-0.0225	-0.0011	0.017	-0.0292	0.012	-0.0082	0.0066	0.0445	0.0347	0.0349	0.0847	-0.0334	0.1031	35.5127	76.7226	-1.8933
11	0.0222	-0.006	-0.0004	0.0213	0.0051	0.0057	0.015	-0.0724	-0.0532	0.044	0.0469	0.0046	-0.0114	-0.0535	0.1227	-0.1071	0.099	0.1032	0.014	-0.0518	-0.0031	31.6458	82.0019	11.9181
12	0.1037	-0.0279	-0.0862	0.0453	-0.0118	0.1055	0.0116	-0.1667	-0.0028	0.1303	0.1045	-0.0006	-0.0142	0.067	0.0966	0.1187	0.0935	0.0208	0.1811	-0.04	-0.0043	39.7788	87.444	26.3529
13	0.0066	0.0015	-0.002	0.0012	0.0011	0.0022	0.0017	0.0006	0.0102	0.0153	0.0023	-0.0057	-0.0184	0.0134	-0.0013	0.1543	-0.0338	0.0169	0.117	-0.1226	0.1124	49.6482	102.6711	21.4199
14	0.0017	-0.0014	-0.0009	0.0003	-0.0002	0.0038	0.0082	-0.0336	-0.014	0.0155	0.0294	-0.014	0.0159	0.0076	0.026	0.1108	0.0856	-0.0649	0.2223	-0.0025	0.0738	51.3804	81.2642	22.6379
15	0.0597	-0.0241	0.0103	0.03	-0.0005	0.0021	0.0005	-0.0485	-0.0274	0.0211	0.0695	-0.0584	-0.0095	0.0814	0.0745	-0.0647	0.0312	-0.042	0.1219	-0.0566	0.0796	57.0597	88.3883	6.7004
16	0.0015	-0.001	-0.0037	0.0063	0.0076	0.0114	0.0034	0.0094	-0.003	-0.0146	0.043	-0.0811	-0.0037	0.0725	0.0265	0.0101	-0.0065	0.0114	0.1358	-0.0397	0.1053	54.2404	89.534	-1.9949

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESID 4:48 )
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESID 49:110 )
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESID 111:211 )
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESID 212:289 )
5	X-RAY DIFFRACTION	5	CHAIN A AND (RESID 290:315 )
6	X-RAY DIFFRACTION	6	CHAIN A AND (RESID 316:354 )
7	X-RAY DIFFRACTION	7	CHAIN A AND (RESID 355:408 )
8	X-RAY DIFFRACTION	8	CHAIN A AND (RESID 409:448 )
9	X-RAY DIFFRACTION	9	CHAIN B AND (RESID 4:71 )
10	X-RAY DIFFRACTION	10	CHAIN B AND (RESID 72:110 )
11	X-RAY DIFFRACTION	11	CHAIN B AND (RESID 111:211 )
12	X-RAY DIFFRACTION	12	CHAIN B AND (RESID 212:303 )
13	X-RAY DIFFRACTION	13	CHAIN B AND (RESID 304:330 )
14	X-RAY DIFFRACTION	14	CHAIN B AND (RESID 331:354 )
15	X-RAY DIFFRACTION	15	CHAIN B AND (RESID 355:408 )
16	X-RAY DIFFRACTION	16	CHAIN B AND (RESID 409:448 )

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