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- PDB-8wna: Crystal structure of GH1 beta-glucosidase Td2F2 E352Q laminaribio... -

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Basic information

Entry
Database: PDB / ID: 8wna
TitleCrystal structure of GH1 beta-glucosidase Td2F2 E352Q laminaribiose complex
Componentsbeta-glucosidase Td2F2
KeywordsHYDROLASE / beta-Glucosidase / E352Q nucleophile mutants / Laminaribiose complex
Function / homologybeta-laminaribiose / MALONIC ACID
Function and homology information
Biological speciesmetagenomes (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 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)52,9967
Polymers51,5621
Non-polymers1,4346
Water6,197344
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.410, 68.416, 95.988
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#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

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Sugars , 2 types, 3 molecules

#2: Polysaccharide beta-D-glucopyranose-(1-3)-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Antimicrobial / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-laminaribiose
DescriptorTypeProgram
DGlcpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5]/1-1/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-glucopyranose-(1-3)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-3DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2122h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(3+1)][b-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 347 molecules

#4: 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 genetically manipulated source
Formula: C3H4O4
#5: 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 genetically manipulated source
Formula: C8H17NO3S / Comment: pH buffer*YM
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 46.15 %
Crystal growTemperature: 303 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: CHES, K/Na tartrate, LiSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: May 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.16→48.42 Å / Num. obs: 155824 / % possible obs: 99.9 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.016 / Rrim(I) all: 0.041 / Χ2: 0.9 / Net I/σ(I): 25.7
Reflection shellResolution: 1.16→1.18 Å / Redundancy: 5 % / Rmerge(I) obs: 0.254 / Mean I/σ(I) obs: 6 / Num. unique obs: 7593 / CC1/2: 0.958 / Rpim(I) all: 0.123 / Rrim(I) all: 0.283 / Χ2: 1.1 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.16→48.42 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.387 / SU ML: 0.019 / Cross valid method: THROUGHOUT / ESU R: 0.031 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16398 7437 4.8 %RANDOM
Rwork0.15074 ---
obs0.1514 148291 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.876 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.16→48.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3475 0 94 344 3913
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0123760
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163373
X-RAY DIFFRACTIONr_angle_refined_deg1.9071.6545149
X-RAY DIFFRACTIONr_angle_other_deg0.6381.5717759
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5115462
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.017530
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.60210529
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1080.2548
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024527
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02926
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_it1.3181.0131818
X-RAY DIFFRACTIONr_mcbond_other1.3161.0121818
X-RAY DIFFRACTIONr_mcangle_it2.0041.8182287
X-RAY DIFFRACTIONr_mcangle_other2.0051.8182288
X-RAY DIFFRACTIONr_scbond_it2.4091.2251942
X-RAY DIFFRACTIONr_scbond_other2.4091.2261943
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4742.1572862
X-RAY DIFFRACTIONr_long_range_B_refined4.31113.074505
X-RAY DIFFRACTIONr_long_range_B_other4.3113.074506
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.16→1.19 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 305 -
Rwork0.228 10977 -
obs--98.92 %

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