PDB-9lpi: Neutron structure of GH1 beta-glucosidase Td2F2 glucose complex a...

ID or keywords:

Entry

Database: PDB / ID: 9lpi

Title

Neutron structure of GH1 beta-glucosidase Td2F2 glucose complex at room temperature

Components

BETA-GLUCOSIDASE

Keywords

HYDROLASE / TIM BARREL / NEUTRON / ROOM-TEMPERATURE

Function / homology

beta-D-glucopyranose / DEUTERATED WATER

Function and homology information

Biological species

metagenome (others)

Method

X-RAY DIFFRACTION / NEUTRON DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.2 Å

Authors

Yano, N. / Arakawa, H. / Lin, C.C. / Ishiwata, A. / Tanaka, K. / Kusaka, K. / Fushinobu, S.

Funding support

Japan, 3items

Organization	Grant number	Country
Japan Society for the Promotion of Science (JSPS)	22K06157	Japan
Japan Society for the Promotion of Science (JSPS)	19H00929	Japan
Japan Society for the Promotion of Science (JSPS)	24H02269	Japan

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: Neutron crystallography of the covalent intermediate of beta-glucosidase reveals remodeling of the catalytic center.
Authors: Yano, N. / Arakawa, H. / Lin, C.C. / Ishiwata, A. / Tanaka, K. / Kusaka, K. / Fushinobu, S.

History

Deposition	Jan 24, 2025	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Oct 29, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9lpi.cif.gz	197.5 KB	Display	PDBx/mmCIF format
PDB format	pdb9lpi.ent.gz	160.3 KB	Display	PDB format
PDBx/mmJSON format	9lpi.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9lpi_validation.pdf.gz	461.6 KB	Display	wwPDB validaton report
Full document	9lpi_full_validation.pdf.gz	461.6 KB	Display
Data in XML	9lpi_validation.xml.gz	11.2 KB	Display
Data in CIF	9lpi_validation.cif.gz	21.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lp/9lpi ftp://data.pdbj.org/pub/pdb/validation_reports/lp/9lpi	HTTPS FTP

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Related structure data

Related structure data	9lphC 9lpvC 9lpxC 9lpyC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#105 - Sep 2008 Ribonuclease A similarity (1) #207 - Mar 2017 Photoactive Yellow Protein similarity (1) #198 - Jun 2016 Beta-galactosidase similarity (1) #75 - Mar 2006 Tissue Factor similarity (1) #77 - May 2006 Glucose Oxidase similarity (1)

Deposited unit

A: BETA-GLUCOSIDASE

hetero molecules

51.2 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)	69.650, 71.090, 97.380
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: 50846.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Sequence refers to UniParc database UPI0002639209. / Source: (gene. exp.) metagenome (others) / Production host:

Escherichia coli (E. coli) / Strain (production host): Rosett TM(DE3) / References: beta-glucosidase

#2: Sugar

ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose

Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₂O₆ / Feature type: SUBJECT OF INVESTIGATION

#3: Chemical

ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES

Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₇NO₃S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM

#4: Chemical

ChemComp-DOD / water

Mass: 18.015 Da / Num. of mol.: 275 / Source method: isolated from a natural source / Formula: D₂O / Feature type: SUBJECT OF INVESTIGATION

Has ligand of interest

Y

Has protein modification

N

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Experiment

Experiment

Method	Number of used crystals
X-RAY DIFFRACTION	1
NEUTRON DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.37 Å³/Da / Density % sol: 48.12 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5 Details: Protein solution: protein 20mg/mL, 5mM Tris pD 8.9 Reservoir solution: 0.1M CHES pD 9.5, 0.940M K/Na tartrate, 5% (w/v) 1-butylpyridinium chloride, 0.2M Li2SO4, 0.2M glucose in heavy water

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID	Serial crystal experiment
1	293	1	N
2	293	1	N

Diffraction source

Source	Site	Beamline	Type	ID	Wavelength (Å)
SYNCHROTRON	Photon Factory	BL-5A		1	1
SPALLATION SOURCE	JPARC MLF	BL-03	J-PARC MLF BEAMLINE BL-03	2	1.86-5.76

Detector

Type	ID	Detector	Date
DECTRIS PILATUS 6M	1	PIXEL	May 15, 2022
iBIX	2	DIFFRACTOMETER	Apr 1, 2022

Radiation

ID	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	SINGLE WAVELENGTH	M	x-ray	1
2	LAUE	L	neutron	2

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1	1
2	1.86	1
3	5.76	1

Reflection

Entry-ID: 9LPI / Net I/σ(I): 14.2

Resolution (Å)	Num. obs	% possible obs (%)	Redundancy (%)	CC_1/2	R_merge(I) obs	R_pim(I) all	Diffraction-ID
1.2-44.3	144269	95.7	6.7	0.998	0.072	0.03	1
1.7-19.74	52857	98.1	7.2	0.984	0.224	0.088	2

Reflection shell

Mean I/σ(I) obs: 2.2

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	Diffraction-ID	% possible all
1.2-1.22	7	0.885	6851	0.73	0.355	1	92.7
1.7-1.76	5.3	0.828	5058	0.428	0.378	2	95.7

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Processing

Refinement

B_iso mean: 23.4 Å² / SU ML: 0.15 / R Free selection details: Random selection / Cross valid method: FREE R-VALUE / Method to determine structure: MOLECULAR REPLACEMENT / Phase error: 15.32 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Stereochemistry target values: ML / Solvent model: FLAT BULK SOLVENT MODEL

Resolution (Å)	Refine-ID	R_factor R_free	R_factor R_work	R_factor obs	Num. reflection R_free	Num. reflection obs	% reflection R_free (%)	% reflection obs (%)	Diffraction-ID
1.2-44.3	X-RAY DIFFRACTION	0.1622	0.1528	0.1533	7202	144184	5	95.42	1
1.7-19.74	NEUTRON DIFFRACTION	0.1695	0.1484	0.1495	2634	52854	4.98	98.18	2

Refinement step

Cycle: LAST / Resolution: 1.2→44.3 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3458	0	25	275	3758

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	7680
X-RAY DIFFRACTION	f_angle_d	1.21	13657
X-RAY DIFFRACTION	f_dihedral_angle_d	13.354	2101
X-RAY DIFFRACTION	f_chiral_restr	0.089	511
X-RAY DIFFRACTION	f_plane_restr	0.008	1553

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 (%)
1.2-1.21	0.283	237	0.2534	4329	X-RAY DIFFRACTION	92
1.21-1.23	0.2664	228	0.2427	4411	X-RAY DIFFRACTION	93
1.23-1.24	0.2401	229	0.2408	4404	X-RAY DIFFRACTION	93
1.24-1.26	0.2359	219	0.2382	4367	X-RAY DIFFRACTION	92
1.26-1.28	0.2237	242	0.2345	4393	X-RAY DIFFRACTION	93
1.28-1.29	0.2288	235	0.2309	4454	X-RAY DIFFRACTION	93
1.29-1.31	0.2884	230	0.2398	4432	X-RAY DIFFRACTION	94
1.31-1.33	0.2433	238	0.2319	4443	X-RAY DIFFRACTION	94
1.33-1.35	0.2336	227	0.2202	4466	X-RAY DIFFRACTION	94
1.35-1.37	0.2209	232	0.2159	4480	X-RAY DIFFRACTION	94
1.37-1.4	0.2047	227	0.2031	4491	X-RAY DIFFRACTION	94
1.4-1.42	0.1993	239	0.1972	4511	X-RAY DIFFRACTION	94
1.42-1.45	0.2293	239	0.1901	4516	X-RAY DIFFRACTION	95
1.45-1.48	0.2096	247	0.1838	4488	X-RAY DIFFRACTION	95
1.48-1.51	0.2068	237	0.1754	4556	X-RAY DIFFRACTION	95
1.51-1.55	0.1773	243	0.1728	4532	X-RAY DIFFRACTION	95
1.55-1.59	0.2035	234	0.1769	4539	X-RAY DIFFRACTION	96
1.59-1.63	0.1973	239	0.1702	4577	X-RAY DIFFRACTION	96
1.63-1.68	0.1678	249	0.1671	4552	X-RAY DIFFRACTION	96
1.68-1.73	0.1828	234	0.1624	4576	X-RAY DIFFRACTION	96
1.73-1.79	0.1784	249	0.1566	4605	X-RAY DIFFRACTION	96
1.79-1.86	0.1609	243	0.1425	4630	X-RAY DIFFRACTION	97
1.86-1.95	0.1481	241	0.1376	4632	X-RAY DIFFRACTION	96
1.95-2.05	0.1387	248	0.1331	4664	X-RAY DIFFRACTION	97
2.05-2.18	0.144	243	0.1299	4715	X-RAY DIFFRACTION	98
2.18-2.35	0.1229	250	0.1298	4691	X-RAY DIFFRACTION	98
2.35-2.59	0.1501	244	0.1305	4770	X-RAY DIFFRACTION	98
2.59-2.96	0.1402	255	0.1385	4801	X-RAY DIFFRACTION	98
2.96-3.73	0.1438	251	0.1275	4874	X-RAY DIFFRACTION	99
3.73-44.3	0.1316	273	0.1345	5083	X-RAY DIFFRACTION	100
1.7-1.73	0.2953	129	0.2648	2507	NEUTRON DIFFRACTION	95
1.73-1.76	0.2688	131	0.2538	2566	NEUTRON DIFFRACTION	96
1.76-1.8	0.2685	137	0.2449	2538	NEUTRON DIFFRACTION	96
1.8-1.84	0.2492	135	0.2202	2574	NEUTRON DIFFRACTION	96
1.84-1.88	0.2095	138	0.2117	2586	NEUTRON DIFFRACTION	97
1.88-1.93	0.2285	144	0.2031	2573	NEUTRON DIFFRACTION	98
1.93-1.98	0.2264	135	0.1912	2623	NEUTRON DIFFRACTION	98
1.98-2.04	0.2005	136	0.1772	2600	NEUTRON DIFFRACTION	98
2.04-2.11	0.2202	133	0.1598	2657	NEUTRON DIFFRACTION	99
2.11-2.18	0.2108	141	0.1466	2668	NEUTRON DIFFRACTION	99
2.18-2.27	0.1545	137	0.1425	2658	NEUTRON DIFFRACTION	100
2.27-2.37	0.1595	142	0.1287	2688	NEUTRON DIFFRACTION	100
2.37-2.5	0.1609	136	0.1206	2674	NEUTRON DIFFRACTION	100
2.5-2.65	0.1465	143	0.1217	2683	NEUTRON DIFFRACTION	100
2.65-2.86	0.1578	140	0.1241	2706	NEUTRON DIFFRACTION	100
2.86-3.14	0.1256	142	0.1188	2697	NEUTRON DIFFRACTION	99
3.14-3.59	0.1342	142	0.1105	2711	NEUTRON DIFFRACTION	99
3.59-4.52	0.1096	149	0.1004	2740	NEUTRON DIFFRACTION	99
4.52-19.74	0.0974	144	0.105	2771	NEUTRON DIFFRACTION	96

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