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- PDB-6m6m: The crystal structure of glycosidase mutant -

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Basic information

Entry
Database: PDB / ID: 6m6m
TitleThe crystal structure of glycosidase mutant
ComponentsBeta-glucosidase
KeywordsHYDROLASE / Glycosidase / Notoginsenoside / Mutant
Function / homology
Function and homology information


scopolin beta-glucosidase activity / beta-glucosidase activity / beta-glucosidase / cellulose catabolic process
Similarity search - Function
Glycoside hydrolase, family 1, beta-glucosidase / Glycosyl hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesKribbella flavida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsWang, R.F.
CitationJournal: To Be Published
Title: Characterization and Structural Elucidation of Enhanced Catalytic Activity upon Engineering Glycosidase KfGH01 for the Production of Vina-ginsenoside R7
Authors: Wang, R.F.
History
DepositionMar 15, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-glucosidase
B: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,9624
Polymers98,7182
Non-polymers2442
Water21,5281195
1
A: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4812
Polymers49,3591
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4812
Polymers49,3591
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.734, 95.432, 93.382
Angle α, β, γ (deg.)90.00, 90.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-glucosidase /


Mass: 49359.059 Da / Num. of mol.: 2 / Mutation: I248F, Y410R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kribbella flavida (strain DSM 17836 / JCM 10339 / NBRC 14399) (bacteria)
Strain: DSM 17836 / JCM 10339 / NBRC 14399 / Gene: Kfla_5268
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: D2PL27, beta-glucosidase
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1195 / 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: 2.38 Å3/Da / Density % sol: 48.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris-HCl (pH 8.5), 0.2 M Magnesium chloride, PEG 8000 (20%, w/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.07→50 Å / Num. obs: 342172 / % possible obs: 99.9 % / Redundancy: 3.7 % / CC1/2: 0.99 / Net I/σ(I): 27.6
Reflection shellResolution: 2.07→2.11 Å / Num. unique obs: 342172 / CC1/2: 0.99

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TA9

3ta9


Resolution: 2.07→32.634 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.39
RfactorNum. reflection% reflection
Rfree0.1782 1985 3.37 %
Rwork0.1339 --
obs0.1354 58888 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.07→32.634 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6965 0 16 1195 8176
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077184
X-RAY DIFFRACTIONf_angle_d0.8759828
X-RAY DIFFRACTIONf_dihedral_angle_d15.24169
X-RAY DIFFRACTIONf_chiral_restr0.0551033
X-RAY DIFFRACTIONf_plane_restr0.0071302
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.08990.18351330.12164035X-RAY DIFFRACTION99
2.0899-2.14640.19341520.12634041X-RAY DIFFRACTION100
2.1464-2.20960.20991390.12264048X-RAY DIFFRACTION100
2.2096-2.28090.1891230.12844083X-RAY DIFFRACTION100
2.2809-2.36240.17621460.12634037X-RAY DIFFRACTION100
2.3624-2.45690.18261380.12984051X-RAY DIFFRACTION100
2.4569-2.56870.19271400.13454067X-RAY DIFFRACTION100
2.5687-2.70410.19181520.144028X-RAY DIFFRACTION100
2.7041-2.87340.19121480.14874084X-RAY DIFFRACTION100
2.8734-3.09510.1861440.14834087X-RAY DIFFRACTION100
3.0951-3.40630.17621390.13694051X-RAY DIFFRACTION100
3.4063-3.89850.15591450.12834079X-RAY DIFFRACTION100
3.8985-4.9090.15431420.12084092X-RAY DIFFRACTION100
4.909-32.6330.16491440.1534120X-RAY DIFFRACTION99

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