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- PDB-7wds: Crystal structures of MeBglD2 in complex with various saccharides -

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Basic information

Entry
Database: PDB / ID: 7wds
TitleCrystal structures of MeBglD2 in complex with various saccharides
ComponentsBeta-glucosidase
KeywordsHYDROLASE / glycoside hydrolase family 1
Function / homology
Function and homology information


beta-glucosidase / beta-glucosidase activity / cellulose catabolic process
Similarity search - Function
Glycoside hydrolase, family 1, beta-glucosidase / Glycoside hydrolase family 1, active site / Glycosyl hydrolases family 1 active site. / Glycosyl hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel ...Glycoside hydrolase, family 1, beta-glucosidase / Glycoside hydrolase family 1, active site / Glycosyl hydrolases family 1 active site. / Glycosyl hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
beta-D-xylopyranose / beta-glucosidase
Similarity search - Component
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsWatanabe, M. / Matsuzawa, T. / Nakamichi, Y. / Akita, H. / Yaoi, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2022
Title: Crystal structure of metagenomic beta-glycosidase MeBglD2 in complex with various saccharides
Authors: Matsuzawa, T. / Watanabe, M. / Nakamichi, Y. / Akita, H. / Yaoi, K.
History
DepositionDec 22, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6775
Polymers52,1851
Non-polymers4924
Water5,296294
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-17 kcal/mol
Surface area16120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)203.169, 203.169, 203.169
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432
Components on special symmetry positions
IDModelComponents
11A-723-

HOH

21A-847-

HOH

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Components

#1: Protein Beta-glucosidase


Mass: 52185.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1E1FFN6, beta-glucosidase
#2: Sugar ChemComp-XYP / beta-D-xylopyranose / beta-D-xylose / D-xylose / xylose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C5H10O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DXylpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-xylopyranoseCOMMON NAMEGMML 1.0
b-D-XylpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.35 Å3/Da / Density % sol: 63.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris-HCl buffer (pH 8.5), 1.2 M lithium sulfate, 0.01 M nickel chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.68→50 Å / Num. obs: 80168 / % possible obs: 99.9 % / Redundancy: 19.3 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 27.8
Reflection shellResolution: 1.68→1.71 Å / Rmerge(I) obs: 0.745 / Num. unique obs: 3894

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XGZ

5xgz


Resolution: 1.68→41.47 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.318 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.019 / ESU R Free: 0.019 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22864 3918 4.9 %RANDOM
Rwork0.16536 ---
obs0.16847 76179 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.144 Å2
Baniso -1Baniso -2Baniso -3
1-7.43 Å2-10.71 Å2-28.81 Å2
2--23.19 Å2-13.27 Å2
3----30.62 Å2
Refinement stepCycle: 1 / Resolution: 1.68→41.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3596 0 30 294 3920
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0133748
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173279
X-RAY DIFFRACTIONr_angle_refined_deg1.9751.6535119
X-RAY DIFFRACTIONr_angle_other_deg1.4931.587562
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9745445
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.52121.159233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.63315542
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2851533
X-RAY DIFFRACTIONr_chiral_restr0.0940.2459
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024293
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02907
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_it3.642.8331777
X-RAY DIFFRACTIONr_mcbond_other3.6392.8311776
X-RAY DIFFRACTIONr_mcangle_it4.1954.2472220
X-RAY DIFFRACTIONr_mcangle_other4.1954.2482221
X-RAY DIFFRACTIONr_scbond_it6.6673.2361969
X-RAY DIFFRACTIONr_scbond_other6.5313.2221961
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.3544.7092886
X-RAY DIFFRACTIONr_long_range_B_refined6.5834.2514453
X-RAY DIFFRACTIONr_long_range_B_other6.56333.9284398
X-RAY DIFFRACTIONr_rigid_bond_restr4.29937024
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.684→1.728 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 270 -
Rwork0.304 5593 -
obs--99.95 %

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