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- PDB-8wn5: Crystal structure of GH1 beta-glucosidase Td2F2 E352Q glucose complex -

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Basic information

Entry
Database: PDB / ID: 8wn5
TitleCrystal structure of GH1 beta-glucosidase Td2F2 E352Q glucose complex
Componentsbeta-glucosidase Td2F2
KeywordsHYDROLASE / beta-Glucosidase / E352Q nucleophile mutants / Glucose complex
Function / homologybeta-D-glucopyranose / MALONIC ACID
Function and homology information
Biological speciesmetagenomes (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLin, C.C. / Lu, T.J. / Fushinobu, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To be published
Title: Structural Basis for Specific Hydrolysis and Synthesis of beta-1-2-glucosidic linkage by Glucose-tolerant beta-glucosidase Td2F2
Authors: Lin, C.C. / Lu, T.J. / Fushinobu, S.
History
DepositionOct 5, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 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 Td2F2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0534
Polymers51,5621
Non-polymers4923
Water5,314295
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.608, 69.240, 96.683
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein beta-glucosidase Td2F2


Mass: 51561.605 Da / Num. of mol.: 1 / Mutation: E352Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenomes (others) / Production host: Escherichia coli (E. coli) / References: beta-glucosidase
#2: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H4O4
#3: 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
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: 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 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.28 Å3/Da / Density % sol: 46.07 %
Crystal growTemperature: 303 K / Method: vapor diffusion, sitting drop / Details: CHES, K/Na tartrate, LiSO4 / PH range: 8.5-9.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→48.42 Å / Num. obs: 73302 / % possible obs: 100 % / Redundancy: 1.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.025 / Rpim(I) all: 0.025 / Rrim(I) all: 0.035 / Χ2: 0.97 / Net I/σ(I): 24.3
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.068 / Mean I/σ(I) obs: 9.6 / Num. unique obs: 3592 / CC1/2: 0.977 / Rpim(I) all: 0.068 / Rrim(I) all: 0.096 / Χ2: 0.68 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→48.42 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.003 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18541 3786 5.2 %RANDOM
Rwork0.1706 ---
obs0.17138 69515 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.278 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å2-0 Å20 Å2
2--0.01 Å2-0 Å2
3----0.8 Å2
Refinement stepCycle: 1 / Resolution: 1.5→48.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3475 0 32 295 3802
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0123661
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163304
X-RAY DIFFRACTIONr_angle_refined_deg1.8431.6495006
X-RAY DIFFRACTIONr_angle_other_deg0.6311.577581
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4815454
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.688529
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.64710522
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0950.2521
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024441
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02907
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1660.7361798
X-RAY DIFFRACTIONr_mcbond_other1.1650.7361798
X-RAY DIFFRACTIONr_mcangle_it1.8321.3232255
X-RAY DIFFRACTIONr_mcangle_other1.8321.3232256
X-RAY DIFFRACTIONr_scbond_it2.0260.9361863
X-RAY DIFFRACTIONr_scbond_other2.0260.9371864
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0481.6282751
X-RAY DIFFRACTIONr_long_range_B_refined4.1118.824257
X-RAY DIFFRACTIONr_long_range_B_other4.1118.824258
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 299 -
Rwork0.232 5082 -
obs--99.98 %

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