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- PDB-8xru: The crystal structure of a GH3 enzyme CcBgl3B with glycerol -

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Basic information

Entry
Database: PDB / ID: 8xru
TitleThe crystal structure of a GH3 enzyme CcBgl3B with glycerol
ComponentsGH3 enzyme CcBgl3B
KeywordsHYDROLASE / GH3 enzyme CcBgl3B / glycerol
Biological speciesCellulosimicrobium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,7209
Polymers245,2713
Non-polymers4496
Water27,2571513
1
A: GH3 enzyme CcBgl3B
B: GH3 enzyme CcBgl3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,9638
Polymers163,5142
Non-polymers4496
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: GH3 enzyme CcBgl3B

C: GH3 enzyme CcBgl3B


Theoretical massNumber of molelcules
Total (without water)163,5142
Polymers163,5142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_757-x+2,y,-z+21
Unit cell
Length a, b, c (Å)162.992, 182.048, 145.284
Angle α, β, γ (deg.)90.00, 102.01, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1589-

HOH

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Components

#1: Protein GH3 enzyme CcBgl3B


Mass: 81757.086 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cellulosimicrobium (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1513 / 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: 4.3 Å3/Da / Density % sol: 71.38 %
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: 2.02→19.85 Å / Num. obs: 266952 / % possible obs: 98.9 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 9.2
Reflection shellResolution: 2.02→2.05 Å / Rmerge(I) obs: 0.628 / Num. unique obs: 12448

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Processing

SoftwareName: PHENIX / Version: (1.18.2_3874: ???) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→19.85 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2354 1998 0.75 %
Rwork0.2054 --
obs0.2057 266868 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.02→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12476 0 26 1513 14015
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713285
X-RAY DIFFRACTIONf_angle_d0.9618165
X-RAY DIFFRACTIONf_dihedral_angle_d30.5741898
X-RAY DIFFRACTIONf_chiral_restr0.0552122
X-RAY DIFFRACTIONf_plane_restr0.0062402
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.070.31881370.296418145X-RAY DIFFRACTION95
2.07-2.130.2881420.257418822X-RAY DIFFRACTION99
2.13-2.190.28111420.238218888X-RAY DIFFRACTION99
2.19-2.260.27321440.226518932X-RAY DIFFRACTION99
2.26-2.340.25321420.213918856X-RAY DIFFRACTION99
2.34-2.430.22671430.203518977X-RAY DIFFRACTION99
2.43-2.540.2691410.199718955X-RAY DIFFRACTION99
2.54-2.680.20341440.197518955X-RAY DIFFRACTION99
2.68-2.850.23821430.201719018X-RAY DIFFRACTION99
2.85-3.060.25951440.205718981X-RAY DIFFRACTION99
3.06-3.370.25591430.20419001X-RAY DIFFRACTION99
3.37-3.860.20681440.188219020X-RAY DIFFRACTION99
3.86-4.850.19781440.178919149X-RAY DIFFRACTION100
4.85-19.850.23091450.215719171X-RAY DIFFRACTION99

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