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- PDB-7w2w: Crystal structure of TxGH116 R786K mutant from Thermoanaerobacter... -

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Basic information

Entry
Database: PDB / ID: 7w2w
TitleCrystal structure of TxGH116 R786K mutant from Thermoanaerobacterium xylanolyticum with glucose
ComponentsGlucosylceramidase
KeywordsHYDROLASE / TxGH116 / beta-glucosidase / mutant / Thermoanaerobacterium xylanolyticum / glucose
Function / homology
Function and homology information


glucosylceramidase / glucosylceramide catabolic process / glucosylceramidase activity / beta-glucosidase activity / carbohydrate metabolic process / metal ion binding / membrane
Similarity search - Function
Glycosyl-hydrolase family 116, catalytic region / Beta-glucosidase GBA2-type / Glycosyl-hydrolase family 116, N-terminal / : / Glycosyl-hydrolase family 116, catalytic region / beta-glucosidase 2, glycosyl-hydrolase family 116 N-term / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
beta-D-glucopyranose / alpha-D-glucopyranose / Glucosylceramidase
Similarity search - Component
Biological speciesThermoanaerobacterium xylanolyticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsHuang, M. / Pengthaisong, S. / Charoenwattanasatien, R. / Jitonnom, J. / Ketudat Cairns, J.R.
Funding support Thailand, 5items
OrganizationGrant numberCountry
Other governmentSuranaree University of Technology Thailand
Other governmentThailand Research Fund Thailand
Other governmentThailand Science Research and Innovation Thailand
Other governmentSynchrotron Light Research Institute (Public Organization) Thailand
Other governmentUniversity of Phayao Thailand
CitationJournal: Catalysts / Year: 2022
Title: Systematic Functional and Computational Analysis of Glucose-Binding Residues in Glycoside Hydrolase Family GH116.
Authors: Huang, M. / Pengthaisong, S. / Charoenwattanasatien, R. / Thinkumrob, N. / Jitonnom, J. / Ketudat Cairns, J.R.
History
DepositionNov 24, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 6, 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: Glucosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,22818
Polymers96,5641
Non-polymers1,66417
Water8,341463
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)177.285, 54.463, 83.074
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Glucosylceramidase


Mass: 96564.422 Da / Num. of mol.: 1 / Mutation: R786K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacterium xylanolyticum (strain ATCC 49914 / DSM 7097 / LX-11) (bacteria)
Strain: ATCC 49914 / DSM 7097 / LX-11 / Gene: Thexy_2211 / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: F6BL85, glucosylceramidase

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Sugars , 2 types, 2 molecules

#2: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#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

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Non-polymers , 5 types, 478 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 463 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.11 Å3/Da / Density % sol: 41.77 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M AMMONIUM SULFATE, 22% PEG 3000, 0.1 M MES, PH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.79→50.01 Å / Num. obs: 75984 / % possible obs: 98.5 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 16.3
Reflection shellResolution: 1.79→1.85 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 6616 / CC1/2: 0.708 / % possible all: 86.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PDB_EXTRACT3.27data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BVU

5bvu


Resolution: 1.79→50.01 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.379 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1855 3615 4.9 %RANDOM
Rwork0.15 ---
obs0.1517 70343 96.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 74.19 Å2 / Biso mean: 22.193 Å2 / Biso min: 6.64 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å2-0 Å20 Å2
2--0.14 Å2-0 Å2
3---0.03 Å2
Refinement stepCycle: final / Resolution: 1.79→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6223 0 106 463 6792
Biso mean--38.18 32.05 -
Num. residues----771
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.026576
X-RAY DIFFRACTIONr_bond_other_d0.0030.026000
X-RAY DIFFRACTIONr_angle_refined_deg1.5271.9458897
X-RAY DIFFRACTIONr_angle_other_deg0.96313865
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6045782
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.925.338311
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.198151090
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2411511
X-RAY DIFFRACTIONr_chiral_restr0.090.2909
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217427
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021540
LS refinement shellResolution: 1.79→1.836 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 180 -
Rwork0.232 3438 -
all-3618 -
obs--64.23 %

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