PDB-9upt: Structure of AtBgl1A, a GH1 beta-Glucosidase from Acetivibrio the...

ID or keywords:

Entry

Database: PDB / ID: 9upt

Title

Structure of AtBgl1A, a GH1 beta-Glucosidase from Acetivibrio thermocellus

Components

Beta-glucosidase A

Keywords

HYDROLASE / beta-Glucosidase / GH1 / Acetivibrio thermocellus

Function / homology

Function and homology information

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

Biological species

Acetivibrio thermocellus ATCC 27405 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.369 Å

Authors

Pitchayatanakorn, P. / Kongsaeree, P.T. / Kongsaeree, P.

Funding support

1items

Citation

Journal: Acs Omega / Year: 2025
Title: Structure-Based Engineering to Improve Thermostability of At Bgl1A beta ‐Glucosidase.
Authors: Pitchayatanakorn, P. / Putthasang, P. / Chomngam, S. / Jongkon, N. / Choowongkomon, K. / Kongsaeree, P. / Fushinobu, S. / Kongsaeree, P.T.

History

Deposition	Apr 29, 2025	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 2, 2025	Provider: repository / Type: Initial release
Revision 1.1	Jul 23, 2025	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9upt.cif.gz	189.5 KB	Display	PDBx/mmCIF format
PDB format	pdb9upt.ent.gz	147.1 KB	Display	PDB format
PDBx/mmJSON format	9upt.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9upt_validation.pdf.gz	430.9 KB	Display	wwPDB validaton report
Full document	9upt_full_validation.pdf.gz	432.2 KB	Display
Data in XML	9upt_validation.xml.gz	19.7 KB	Display
Data in CIF	9upt_validation.cif.gz	26.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/up/9upt ftp://data.pdbj.org/pub/pdb/validation_reports/up/9upt	HTTPS FTP

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Related structure data

Related structure data	5ogzS S: Starting model for refinement
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Experimental dataset #1	Data reference: 10.51093/xrd-00191 / Data set type: diffraction image data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Beta-glucosidase A

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	158.270, 158.270, 53.962
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	168
Space group name H-M	P6

#1: Protein	Beta-glucosidase A / Beta-D-glucoside glucohydrolase / Cellobiase / Gentiobiase Mass: 53849.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acetivibrio thermocellus ATCC 27405 (bacteria) Gene: bglA, Cthe_0212 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P26208, beta-glucosidase
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	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: 3.62 Å³/Da / Density % sol: 66.05 %
Crystal grow	Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 0.1 M HEPES pH 7.2, 10% 2-propanol, 20% PEG 4000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
Detector	Type: RAYONIX MX300-HS / Detector: CCD / Date: Nov 13, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.369→79.26 Å / Num. obs: 31219 / % possible obs: 98.3 % / Redundancy: 1.9 % / CC_1/2: 0.999 / Net I/σ(I): 10.9
Reflection shell	Resolution: 2.37→2.46 Å / Num. unique obs: 3319 / CC_1/2: 0.799 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0419	refinement
HKL-2000		data reduction
HKL-2000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5OGZ

5ogz

Resolution: 2.369→79.26 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.952 / SU B: 6.401 / SU ML: 0.144 / Cross valid method: FREE R-VALUE / ESU R: 0.21 / ESU R Free: 0.185
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.215	1638	5.247 %
R_work	0.1727	29581	-
all	0.175	-	-
obs	-	31219	98.25 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 47.407 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.263 Å²	-0.631 Å²	-0 Å²
2-	-	-1.263 Å²	0 Å²
3-	-	-	4.096 Å²

Refinement step

Cycle: LAST / Resolution: 2.369→79.26 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3641	0	6	55	3702

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	3748
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	3463
X-RAY DIFFRACTION	r_angle_refined_deg	1.787	1.821	5070
X-RAY DIFFRACTION	r_angle_other_deg	0.616	1.773	8002
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.977	5	446
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	6.573	5	15
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.541	10	641
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.415	10	185
X-RAY DIFFRACTION	r_chiral_restr	0.087	0.2	523
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	4383
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	883
X-RAY DIFFRACTION	r_nbd_refined	0.227	0.2	723
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.192	0.2	3087
X-RAY DIFFRACTION	r_nbtor_refined	0.193	0.2	1846
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.084	0.2	1926
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.151	0.2	96
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.043	0.2	7
X-RAY DIFFRACTION	r_nbd_other	0.14	0.2	28
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.157	0.2	5
X-RAY DIFFRACTION	r_mcbond_it	3.96	4.49	1787
X-RAY DIFFRACTION	r_mcbond_other	3.96	4.49	1787
X-RAY DIFFRACTION	r_mcangle_it	5.485	8.066	2232
X-RAY DIFFRACTION	r_mcangle_other	5.484	8.067	2233
X-RAY DIFFRACTION	r_scbond_it	5.162	4.99	1961
X-RAY DIFFRACTION	r_scbond_other	5.161	4.991	1962
X-RAY DIFFRACTION	r_scangle_it	7.743	8.887	2838
X-RAY DIFFRACTION	r_scangle_other	7.742	8.887	2839
X-RAY DIFFRACTION	r_lrange_it	8.971	41.718	4205
X-RAY DIFFRACTION	r_lrange_other	8.972	41.723	4204

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.369-2.43	0.297	132	0.275	2200	0.276	2334	0.947	0.946	99.9143	0.263
2.43-2.497	0.27	109	0.252	2145	0.253	2255	0.944	0.953	99.9557	0.237
2.497-2.569	0.298	105	0.245	2111	0.248	2216	0.947	0.959	100	0.23
2.569-2.648	0.25	113	0.228	2013	0.229	2127	0.961	0.967	99.953	0.208
2.648-2.735	0.3	111	0.241	1681	0.245	2096	0.949	0.966	85.4962	0.212
2.735-2.83	0.249	114	0.203	1906	0.206	2020	0.957	0.976	100	0.181
2.83-2.937	0.257	93	0.193	1836	0.196	1929	0.951	0.977	100	0.175
2.937-3.057	0.287	82	0.192	1791	0.196	1873	0.954	0.977	100	0.174
3.057-3.193	0.224	108	0.173	1695	0.176	1803	0.968	0.981	100	0.16
3.193-3.348	0.23	115	0.177	1614	0.18	1729	0.969	0.981	100	0.168
3.348-3.529	0.262	70	0.169	1328	0.174	1626	0.967	0.985	85.9779	0.163
3.529-3.743	0.19	67	0.17	1475	0.171	1542	0.976	0.985	100	0.169
3.743-4	0.19	68	0.161	1403	0.162	1473	0.982	0.987	99.8642	0.166
4-4.32	0.179	70	0.15	1288	0.152	1361	0.978	0.988	99.7796	0.161
4.32-4.731	0.184	60	0.122	1199	0.124	1261	0.983	0.991	99.8414	0.135
4.731-5.287	0.169	87	0.128	1069	0.131	1157	0.987	0.991	99.9136	0.144
5.287-6.1	0.21	46	0.159	973	0.161	1019	0.974	0.987	100	0.179
6.1-7.46	0.152	37	0.153	817	0.153	855	0.988	0.987	99.883	0.178
7.46-10.504	0.192	37	0.128	652	0.131	690	0.98	0.989	99.8551	0.161
10.504-79.26	0.163	14	0.219	385	0.217	408	0.987	0.969	97.7941	0.346

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