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- PDB-8xrv: The crystal structure of a GH3 enzyme CcBgl3B with glucose -

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Basic information

Entry
Database: PDB / ID: 8xrv
TitleThe crystal structure of a GH3 enzyme CcBgl3B with glucose
ComponentsGH3 enzyme CcBgl3B
KeywordsHYDROLASE / GH3 enzyme CcBgl3B / glucose
Function / homologybeta-D-glucopyranose
Function and homology information
Biological speciesCellulosimicrobium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSu, J.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171255 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: A trapped covalent intermediate as a key catalytic element in the hydrolysis of a GH3 beta-glucosidase: An X-ray crystallographic and biochemical study.
Authors: Hu, C. / Wang, Y. / Wang, W. / Cui, W. / Jia, X. / Mayo, K.H. / Zhou, Y. / Su, J. / Yuan, Y.
History
DepositionJan 8, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GH3 enzyme CcBgl3B
B: GH3 enzyme CcBgl3B
C: GH3 enzyme CcBgl3B
F: GH3 enzyme CcBgl3B
D: GH3 enzyme CcBgl3B
E: GH3 enzyme CcBgl3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)491,86418
Polymers490,5436
Non-polymers1,32112
Water39,9392217
1
A: GH3 enzyme CcBgl3B
B: GH3 enzyme CcBgl3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,9556
Polymers163,5142
Non-polymers4404
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6410 Å2
ΔGint-35 kcal/mol
Surface area47600 Å2
MethodPISA
2
C: GH3 enzyme CcBgl3B
F: GH3 enzyme CcBgl3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,9556
Polymers163,5142
Non-polymers4404
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6190 Å2
ΔGint-34 kcal/mol
Surface area47950 Å2
MethodPISA
3
D: GH3 enzyme CcBgl3B
hetero molecules

E: GH3 enzyme CcBgl3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,9556
Polymers163,5142
Non-polymers4404
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area6080 Å2
ΔGint-34 kcal/mol
Surface area48090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.330, 177.574, 265.787
Angle α, β, γ (deg.)90.00, 100.86, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
GH3 enzyme CcBgl3B


Mass: 81757.086 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cellulosimicrobium (bacteria) / Production host: Escherichia coli (E. coli)
#2: Sugar
ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H12O6
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
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2217 / 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: 3.86 Å3/Da / Density % sol: 68.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97775 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97775 Å / Relative weight: 1
ReflectionResolution: 2.4→19.97 Å / Num. obs: 288030 / % possible obs: 99.5 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 6.9
Reflection shellResolution: 2.4→2.44 Å / Rmerge(I) obs: 0.684 / Num. unique obs: 14283

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Processing

SoftwareName: PHENIX / Version: (1.18.2_3874: ???) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→19.97 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2153 1999 0.69 %
Rwork0.1761 --
obs0.1763 287964 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33578 0 78 2217 35873
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00834622
X-RAY DIFFRACTIONf_angle_d1.1147356
X-RAY DIFFRACTIONf_dihedral_angle_d28.6554926
X-RAY DIFFRACTIONf_chiral_restr0.065490
X-RAY DIFFRACTIONf_plane_restr0.0076258
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.30641440.257220452X-RAY DIFFRACTION100
2.46-2.530.33031410.252620299X-RAY DIFFRACTION100
2.53-2.60.28461430.234620377X-RAY DIFFRACTION100
2.6-2.680.30211430.22220438X-RAY DIFFRACTION100
2.68-2.780.27771420.207420296X-RAY DIFFRACTION100
2.78-2.890.23011420.198920436X-RAY DIFFRACTION100
2.89-3.020.24831440.194620524X-RAY DIFFRACTION100
3.02-3.180.24591430.192320398X-RAY DIFFRACTION100
3.18-3.380.23151420.189920385X-RAY DIFFRACTION100
3.38-3.640.21841430.169620444X-RAY DIFFRACTION99
3.64-40.19351430.156920413X-RAY DIFFRACTION100
4-4.580.16021410.142420447X-RAY DIFFRACTION99
4.58-5.740.19181430.151720407X-RAY DIFFRACTION99
5.74-19.970.17131450.152920649X-RAY DIFFRACTION99

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