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- PDB-9lpv: Neutron structure of GH1 beta-glucosidase Td2F2 2F-Glc complex at... -

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Basic information

Entry
Database: PDB / ID: 9lpv
TitleNeutron structure of GH1 beta-glucosidase Td2F2 2F-Glc complex at room temperature
ComponentsBETA-GLUCOSIDASE
KeywordsHYDROLASE / TIM BARREL / NEUTRON / ROOM-TEMPERATURE
Function / homologyDEUTERATED WATER / 2-deoxy-2-fluoro-alpha-D-glucopyranose
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å
AuthorsYano, N. / Arakawa, H. / Lin, C.C. / Ishiwata, A. / Tanaka, K. / Kusaka, K. / Fushinobu, S.
Funding support Japan, 3items
OrganizationGrant numberCountry
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
CitationJournal: 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
DepositionJan 26, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA-GLUCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2363
Polymers50,8471
Non-polymers3892
Water5,477304
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.540, 71.230, 97.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#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-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.: 1 / Source method: obtained synthetically / Formula: C6H11FO5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-Glcp2fluoroIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#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.: 304 / Source method: isolated from a natural source / Formula: D2O / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.9
Details: Protein solution: protein reacted 2-deoxy-2-fluoro glucoside 30mg/mL, 5mM Tris pD 8.9 Reservoir solution : 0.1M CHES pD 9.5, 0.890M K/Na tartrate, 5% (w/v) 1-butylpyridinium chloride, 0.2M Li2SO4, in heavy water

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
12931N
22931N
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-5A11
SPALLATION SOURCEJPARC MLF BL-03J-PARC MLF BEAMLINE BL-0321.86-5.76
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELFeb 18, 2023
iBIX2DIFFRACTOMETERJan 17, 2023
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2LAUELneutron2
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.861
35.761
Reflection

Entry-ID: 9LPV

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Biso Wilson estimate (Å2)CC1/2Rmerge(I) obsRpim(I) allDiffraction-IDNet I/σ(I)
1.32-44.2911095297.76.6140.9980.0780.032113.5
1.7-20.075300798.57.60.9910.1840.07122
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allDiffraction-ID% possible all
1.32-1.346.60.8432.153300.7460.351195.6
1.7-1.765.50.76251390.5560.343297

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Processing

Refinement

SU ML: 0.1404 / R Free selection details: Random selection / Cross valid method: FREE R-VALUE / Method to determine structure: MOLECULAR REPLACEMENT / Phase error: 15.6979 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 / Solvent model: FLAT BULK SOLVENT MODEL

Resolution (Å)Refine-IDBiso mean (Å2)Rfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection RworkNum. reflection obs% reflection Rfree (%)% reflection obs (%)Diffraction-IDσ(F)
1.32-44.29X-RAY DIFFRACTION20.440.160.14850.149155321053451108774.9997.4611.34
1.7-20.07NEUTRON DIFFRACTION0.16980.15480.15552629530054.9698.62
Refinement stepCycle: LAST / Resolution: 1.32→44.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3458 0 24 304 3786
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00983586
X-RAY DIFFRACTIONf_angle_d1.05364897
X-RAY DIFFRACTIONf_chiral_restr0.0863509
X-RAY DIFFRACTIONf_plane_restr0.0132728
X-RAY DIFFRACTIONf_dihedral_angle_d12.96861269
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.32-1.330.29011900.26853375X-RAY DIFFRACTION95.3
1.33-1.350.27561690.25663397X-RAY DIFFRACTION95.3
1.35-1.370.29391800.25183419X-RAY DIFFRACTION95.46
1.37-1.380.22131860.24363391X-RAY DIFFRACTION95.72
1.38-1.40.22071840.22273416X-RAY DIFFRACTION95.67
1.4-1.420.22361800.22123415X-RAY DIFFRACTION95.61
1.42-1.440.22441870.21343412X-RAY DIFFRACTION96.23
1.44-1.460.2031770.20263434X-RAY DIFFRACTION96.19
1.46-1.490.20551810.19083447X-RAY DIFFRACTION96.06
1.49-1.510.19751790.18913467X-RAY DIFFRACTION96.76
1.51-1.540.21890.18093418X-RAY DIFFRACTION96.91
1.54-1.560.20821740.18373472X-RAY DIFFRACTION96.89
1.56-1.60.20151730.1833480X-RAY DIFFRACTION96.92
1.6-1.630.21950.17753473X-RAY DIFFRACTION97.14
1.63-1.660.16471660.17783509X-RAY DIFFRACTION97.43
1.66-1.70.18581970.17483479X-RAY DIFFRACTION97.45
1.7-1.740.1951900.17153502X-RAY DIFFRACTION97.44
1.74-1.790.18671750.16013497X-RAY DIFFRACTION97.71
1.79-1.840.16571860.14913515X-RAY DIFFRACTION97.96
1.84-1.90.16791810.14343526X-RAY DIFFRACTION98.2
1.9-1.970.16261850.1443528X-RAY DIFFRACTION98.02
1.97-2.050.15591900.13913555X-RAY DIFFRACTION98.55
2.05-2.140.14211900.14013567X-RAY DIFFRACTION98.84
2.14-2.260.1481850.13183589X-RAY DIFFRACTION98.82
2.26-2.40.14831770.12793608X-RAY DIFFRACTION99.01
2.4-2.580.15441930.13123598X-RAY DIFFRACTION99.27
2.58-2.840.14411900.13993641X-RAY DIFFRACTION99.53
2.84-3.250.14011940.13943651X-RAY DIFFRACTION99.48
3.26-4.10.13471870.1173702X-RAY DIFFRACTION99.62
4.1-44.290.13122020.13223862X-RAY DIFFRACTION99.88

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