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- PDB-9lpy: X-ray structure of GH1 beta-glucosidase Td2F2 2F-Glc complex at c... -

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Basic information

Entry
Database: PDB / ID: 9lpy
TitleX-ray structure of GH1 beta-glucosidase Td2F2 2F-Glc complex at cryogenic temperature
ComponentsBETA-GLUCOSIDASE
KeywordsHYDROLASE / TIM BARREL / CRYOGENIC-TEMPERATURE
Function / homology2-deoxy-2-fluoro-alpha-D-glucopyranose
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.11 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)51,5367
Polymers50,8471
Non-polymers6896
Water7,206400
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint-2 kcal/mol
Surface area15940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.732, 69.788, 95.986
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

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Protein / Sugars , 2 types, 2 molecules A

#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

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Non-polymers , 4 types, 405 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.9
Details: Protein solution: protein reacted 2-deoxy-2-fluoro glucoside 20mg/mL, 5mM Tris pD 8.9 Reservoir solution: 0.1M CHES pD 9.5, 0.935M K/Na tartrate, 5% (w/v) 1-butylpyridinium chloride, 0.2M Li2SO4, in heavy water

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.11→48.97 Å / Num. obs: 182060 / % possible obs: 100 % / Redundancy: 12.8 % / Biso Wilson estimate: 7.19 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.046 / Net I/σ(I): 2.1
Reflection shellResolution: 1.11→1.13 Å / Redundancy: 11.7 % / Rmerge(I) obs: 1.295 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 8940 / CC1/2: 0.724 / Rpim(I) all: 0.392 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSJan 10, 2022data reduction
Aimless0.7.7data scaling
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.11→48.97 Å / SU ML: 0.0946 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.1263
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.176 9096 5 %Random selection
Rwork0.164 172844 --
obs0.1645 181940 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.95 Å2
Refinement stepCycle: LAST / Resolution: 1.11→48.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3467 0 43 400 3910
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00483734
X-RAY DIFFRACTIONf_angle_d0.88295111
X-RAY DIFFRACTIONf_chiral_restr0.0796526
X-RAY DIFFRACTIONf_plane_restr0.0095683
X-RAY DIFFRACTIONf_dihedral_angle_d5.9086534
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.11-1.120.23493250.23835683X-RAY DIFFRACTION100
1.12-1.140.2663030.23325700X-RAY DIFFRACTION99.97
1.14-1.150.23542720.22255721X-RAY DIFFRACTION99.98
1.15-1.160.23262990.21635737X-RAY DIFFRACTION99.97
1.16-1.180.20882920.21235706X-RAY DIFFRACTION99.98
1.18-1.20.23583050.21045690X-RAY DIFFRACTION100
1.2-1.210.23053190.2075697X-RAY DIFFRACTION100
1.21-1.230.21033160.20915694X-RAY DIFFRACTION100
1.23-1.250.21782700.20525756X-RAY DIFFRACTION99.98
1.25-1.270.20082820.20275767X-RAY DIFFRACTION100
1.27-1.290.21013100.19785682X-RAY DIFFRACTION100
1.29-1.320.21953180.19595714X-RAY DIFFRACTION100
1.32-1.340.19413390.19325698X-RAY DIFFRACTION99.98
1.34-1.370.20172980.18325726X-RAY DIFFRACTION100
1.37-1.40.18223150.17665748X-RAY DIFFRACTION100
1.4-1.430.1872810.17075719X-RAY DIFFRACTION100
1.43-1.470.18523120.16385725X-RAY DIFFRACTION99.98
1.47-1.510.16253000.15815739X-RAY DIFFRACTION99.93
1.51-1.550.1683080.15515767X-RAY DIFFRACTION99.98
1.55-1.60.17873090.15535738X-RAY DIFFRACTION99.98
1.6-1.660.17373120.15725749X-RAY DIFFRACTION99.97
1.66-1.720.16053280.15235716X-RAY DIFFRACTION99.97
1.72-1.80.1572910.15035803X-RAY DIFFRACTION100
1.8-1.90.15963000.1415773X-RAY DIFFRACTION99.97
1.9-2.020.14753130.14085810X-RAY DIFFRACTION100
2.02-2.170.1613060.14275791X-RAY DIFFRACTION100
2.17-2.390.1482960.1455845X-RAY DIFFRACTION99.98
2.39-2.740.17552810.15665886X-RAY DIFFRACTION99.92
2.74-3.450.15363150.14745899X-RAY DIFFRACTION99.98
3.45-48.970.17172810.15966165X-RAY DIFFRACTION99.86

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