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- PDB-8xrx: The crystal structure of a GH3 enzyme CcBgl3B with glucose and ge... -

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Basic information

Entry
Database: PDB / ID: 8xrx
TitleThe crystal structure of a GH3 enzyme CcBgl3B with glucose and gentiobiose
ComponentsGH3 enzyme CcBgl3B
KeywordsHYDROLASE / GH3 enzyme CcBgl3B / glucose / gentiobiose
Function / homologybeta-D-glucopyranose / alpha-D-glucopyranose
Function and homology information
Biological speciesCellulosimicrobium cellulans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSu, J.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)492,35018
Polymers490,5436
Non-polymers1,80812
Water7,260403
1
A: GH3 enzyme CcBgl3B
B: GH3 enzyme CcBgl3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,2977
Polymers163,5142
Non-polymers7835
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7220 Å2
ΔGint-31 kcal/mol
Surface area47730 Å2
MethodPISA
2
C: GH3 enzyme CcBgl3B
D: GH3 enzyme CcBgl3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,1176
Polymers163,5142
Non-polymers6034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6600 Å2
ΔGint-36 kcal/mol
Surface area48150 Å2
MethodPISA
3
E: GH3 enzyme CcBgl3B
F: GH3 enzyme CcBgl3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,9375
Polymers163,5142
Non-polymers4223
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint-35 kcal/mol
Surface area44930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.095, 183.009, 269.154
Angle α, β, γ (deg.)90.00, 100.59, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 6 molecules ABCDEF

#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 cellulans (bacteria)
Production host: Escherichia coli (E. coli)

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Sugars , 3 types, 6 molecules

#2: Polysaccharide beta-D-glucopyranose-(1-6)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 3 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpb1-6DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5]/1-1/a6-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(6+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#4: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2 / 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
#5: 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
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

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Non-polymers , 2 types, 409 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 4.02 Å3/Da / Density % sol: 69.44 %
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: NFPSS / Beamline: BL18U / Wavelength: 0.97538 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97538 Å / Relative weight: 1
ReflectionResolution: 2.5→19.95 Å / Num. obs: 264973 / % possible obs: 99 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 8.2
Reflection shellResolution: 2.5→2.54 Å / Rmerge(I) obs: 0.538 / Num. unique obs: 11550

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Processing

SoftwareName: PHENIX / Version: (1.10.1_2155: ???) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→19.948 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2295 2000 0.75 %
Rwork0.1965 --
obs0.1967 264944 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→19.948 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32609 0 110 403 33122
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00933677
X-RAY DIFFRACTIONf_angle_d0.9646082
X-RAY DIFFRACTIONf_dihedral_angle_d19.87119843
X-RAY DIFFRACTIONf_chiral_restr0.0595345
X-RAY DIFFRACTIONf_plane_restr0.0076086
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.56250.35861340.298317573X-RAY DIFFRACTION93
2.5625-2.63160.32381420.274818775X-RAY DIFFRACTION100
2.6316-2.70880.29271440.262918887X-RAY DIFFRACTION100
2.7088-2.79610.29961430.251718831X-RAY DIFFRACTION100
2.7961-2.89570.25871440.244718873X-RAY DIFFRACTION100
2.8957-3.01130.28221440.237918855X-RAY DIFFRACTION100
3.0113-3.14780.27191430.229918901X-RAY DIFFRACTION100
3.1478-3.31310.2471430.222918867X-RAY DIFFRACTION100
3.3131-3.51960.26271430.207518842X-RAY DIFFRACTION100
3.5196-3.78960.21761440.181618885X-RAY DIFFRACTION100
3.7896-4.16780.17911440.161718811X-RAY DIFFRACTION99
4.1678-4.76380.1791430.150418878X-RAY DIFFRACTION100
4.7638-5.9750.20011440.162518932X-RAY DIFFRACTION100
5.975-19.9480.18471450.166219034X-RAY DIFFRACTION99

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