PDB-9lph: Neutron structure of GH1 beta-glucosidase Td2F2 ligand-free form ...

ID or keywords:

Entry

Database: PDB / ID: 9lph

Title

Neutron structure of GH1 beta-glucosidase Td2F2 ligand-free form at room temperature

Components

BETA-GLUCOSIDASE

Keywords

HYDROLASE / TIM BARREL / beta-glucosidase / Neutron / room-temperature

Function / homology

DEUTERATED WATER

Function and homology information

Biological species

metagenome (others)

Method

X-RAY DIFFRACTION / NEUTRON DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.19 Å

Authors

Yano, N. / 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

-
Download

PDBx/mmCIF format	9lph.cif.gz	187.8 KB	Display	PDBx/mmCIF format
PDB format	pdb9lph.ent.gz	151.6 KB	Display	PDB format
PDBx/mmJSON format	9lph.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	9lph_validation.pdf.gz	449.8 KB	Display	wwPDB validaton report
Full document	9lph_full_validation.pdf.gz	449.7 KB	Display
Data in XML	9lph_validation.xml.gz	11.3 KB	Display
Data in CIF	9lph_validation.cif.gz	22.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lp/9lph ftp://data.pdbj.org/pub/pdb/validation_reports/lp/9lph	HTTPS FTP

-
Related structure data

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

-
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)

Deposited unit

A: BETA-GLUCOSIDASE

hetero molecules

51.1 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)	69.720, 71.030, 97.290
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): Rosetta TM (DE3) / References: beta-glucosidase
#2: Chemical	ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES Mass: 207.290 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C₈H₁₇NO₃S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Chemical	ChemComp-DOD / water Mass: 18.015 Da / Num. of mol.: 346 / Source method: isolated from a natural source / Formula: D₂O / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interest	Y
Has protein modification	N

-
Experiment

Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.37 Å³/Da / Density % sol: 48.08 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5 Details: Protein solution: protein 20mg/mL, 5mM Tris-DCl (pD 8.9), Reservoir solution: 0.1M CHES (pD 9.5), 0.912M K/Na tartrate, 5% (w/v) 1-butylpyridinium chloride, 0.2M Li2SO4 in heavy water

-
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	2.28-6.19

Detector

Type	ID	Detector	Date
DECTRIS PILATUS 6M	1	PIXEL	Oct 20, 2021
iBIX	2	DIFFRACTOMETER	Jun 29, 2021

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	2.28	1
3	6.19	1

Reflection

Entry-ID: 9LPH / Observed criterion σ(F): -3 / Observed criterion σ(I): -3

Resolution (Å)	Num. obs	% possible obs (%)	Redundancy (%)	CC_1/2	R_merge(I) obs	R_pim(I) all	Diffraction-ID	Net I/σ(I)
1.19-44.3	154133	99.6	6.6	0.998	0.079	0.033	1	11.4
1.8-22.15	45104	99.1	8	0.983	0.25	0.093	2	8.6

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	Diffraction-ID	% possible all	Mean I/σ(I) obs
1.19-1.21	6.4	0.829	7472	0.755	0.347	1	98.6
1.8-1.86	6.3	0.972	4400	0.466	0.41	2	98.3	1.7

-
Processing

Refinement

SU ML: 0.16 / R Free selection details: Random selection / Cross valid method: FREE R-VALUE / Method to determine structure: MOLECULAR REPLACEMENT / Phase error: 15.43 / 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	B_iso mean (Å²)	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
1.19-44.3	X-RAY DIFFRACTION	22.95	0.1676	0.1524	0.1532	7694	154041	4.99	99.5	1
1.8-22.15	NEUTRON DIFFRACTION		0.1732	0.1492	0.1504	2256	45096	5	99.23	2

Refinement step

Cycle: LAST / Resolution: 1.19→44.3 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3458	0	13	346	3817

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	3575
X-RAY DIFFRACTION	f_angle_d	1.003	4882
X-RAY DIFFRACTION	f_dihedral_angle_d	14.077	1273
X-RAY DIFFRACTION	f_chiral_restr	0.082	506
X-RAY DIFFRACTION	f_plane_restr	0.013	727

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 (%)
1.19-1.2	0.2389	256	0.2522	4764	X-RAY DIFFRACTION	98
1.2-1.22	0.2473	250	0.2464	4777	X-RAY DIFFRACTION	99
1.22-1.23	0.2409	258	0.2482	4782	X-RAY DIFFRACTION	99
1.23-1.25	0.2679	249	0.2401	4803	X-RAY DIFFRACTION	98
1.25-1.26	0.2633	249	0.2378	4773	X-RAY DIFFRACTION	99
1.26-1.28	0.2402	250	0.2391	4806	X-RAY DIFFRACTION	99
1.28-1.3	0.2182	257	0.2317	4827	X-RAY DIFFRACTION	99
1.3-1.32	0.2097	246	0.2309	4807	X-RAY DIFFRACTION	99
1.32-1.34	0.2194	250	0.2152	4833	X-RAY DIFFRACTION	99
1.34-1.36	0.211	253	0.2121	4853	X-RAY DIFFRACTION	100
1.36-1.39	0.2366	265	0.2052	4802	X-RAY DIFFRACTION	99
1.39-1.41	0.2358	245	0.1966	4831	X-RAY DIFFRACTION	99
1.41-1.44	0.1915	252	0.1925	4866	X-RAY DIFFRACTION	99
1.44-1.47	0.1894	259	0.1861	4831	X-RAY DIFFRACTION	100
1.47-1.5	0.171	251	0.1859	4871	X-RAY DIFFRACTION	100
1.5-1.53	0.2064	263	0.1793	4872	X-RAY DIFFRACTION	100
1.53-1.57	0.171	256	0.1788	4859	X-RAY DIFFRACTION	100
1.57-1.62	0.188	251	0.1782	4916	X-RAY DIFFRACTION	100
1.62-1.66	0.1775	259	0.1674	4863	X-RAY DIFFRACTION	100
1.66-1.72	0.1909	255	0.1652	4890	X-RAY DIFFRACTION	100
1.72-1.78	0.1506	251	0.1609	4904	X-RAY DIFFRACTION	100
1.78-1.85	0.1696	268	0.1475	4883	X-RAY DIFFRACTION	100
1.8-1.84	0.3125	127	0.2756	2625	X-RAY DIFFRACTION	98
1.85-1.93	0.1584	253	0.1441	4944	X-RAY DIFFRACTION	100
1.93-2.03	0.1524	263	0.1409	4901	X-RAY DIFFRACTION	100
2.03-2.16	0.1397	257	0.1346	4932	X-RAY DIFFRACTION	100
2.16-2.33	0.1419	265	0.1325	4954	X-RAY DIFFRACTION	100
2.33-2.56	0.1556	261	0.1308	4952	X-RAY DIFFRACTION	100
2.56-2.93	0.1618	258	0.1401	4985	X-RAY DIFFRACTION	100
2.93-3.7	0.1545	266	0.1269	5040	X-RAY DIFFRACTION	100
3.7-44.3	0.1438	278	0.1212	5226	X-RAY DIFFRACTION	100
1.84-1.88	0.2968	140	0.2625	2610	NEUTRON DIFFRACTION	98
1.88-1.93	0.2662	141	0.2419	2610	NEUTRON DIFFRACTION	99
1.93-1.98	0.2603	137	0.226	2640	NEUTRON DIFFRACTION	99
1.98-2.04	0.226	146	0.2127	2627	NEUTRON DIFFRACTION	99
2.04-2.11	0.2347	133	0.1949	2660	NEUTRON DIFFRACTION	99
2.11-2.18	0.2018	149	0.1817	2671	NEUTRON DIFFRACTION	100
2.18-2.27	0.1778	136	0.1708	2665	NEUTRON DIFFRACTION	100
2.27-2.37	0.19	139	0.1558	2687	NEUTRON DIFFRACTION	100
2.37-2.5	0.1995	147	0.1398	2678	NEUTRON DIFFRACTION	100
2.5-2.65	0.1667	135	0.1339	2685	NEUTRON DIFFRACTION	100
2.65-2.86	0.1539	145	0.1288	2702	NEUTRON DIFFRACTION	100
2.86-3.14	0.1418	145	0.1185	2708	NEUTRON DIFFRACTION	100
3.14-3.6	0.1294	145	0.1085	2726	NEUTRON DIFFRACTION	100
3.6-4.52	0.1102	144	0.0933	2772	NEUTRON DIFFRACTION	100
4.52-22.15	0.0976	147	0.0883	2774	NEUTRON DIFFRACTION	96

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi