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- PDB-4r27: Crystal structure of beta-glycosidase BGL167 -

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Basic information

Entry
Database: PDB / ID: 4r27
TitleCrystal structure of beta-glycosidase BGL167
ComponentsGlycoside hydrolase
KeywordsHYDROLASE / Glycoside hydrolase
Function / homology
Function and homology information


Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / carbohydrate catabolic process / beta-glucosidase activity / cytosol
Similarity search - Function
Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesMicrobacterium sp. Gsoil167 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsPark, S.J. / Choi, J.M. / Kyeong, H.H. / Kim, S.G. / Kim, H.S.
CitationJournal: Chembiochem / Year: 2015
Title: Rational design of a beta-glycosidase with high regiospecificity for triterpenoid tailoring
Authors: Park, S.J. / Choi, J.M. / Kyeong, H.H. / Kim, S.G. / Kim, H.S.
History
DepositionAug 9, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycoside hydrolase
B: Glycoside hydrolase


Theoretical massNumber of molelcules
Total (without water)95,6132
Polymers95,6132
Non-polymers00
Water1,22568
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Glycoside hydrolase


Theoretical massNumber of molelcules
Total (without water)47,8061
Polymers47,8061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Glycoside hydrolase


Theoretical massNumber of molelcules
Total (without water)47,8061
Polymers47,8061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.498, 146.940, 53.041
Angle α, β, γ (deg.)90.00, 101.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glycoside hydrolase / beta-Glycosidase


Mass: 47806.281 Da / Num. of mol.: 2 / Mutation: UNP residues 5-425
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Microbacterium sp. Gsoil167 (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: L0ELG0, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O

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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: 1.93 Å3/Da / Density % sol: 36.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5
Details: 36% MPD-PEG 1000-PEG 3350 mixture, 55mM calcium chloride, pH 7.5, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 21, 2013
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.03→50 Å / Num. all: 45495 / Num. obs: 44261 / % possible obs: 97.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.03→2.07 Å / % possible all: 98.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CMJ

3cmj


Resolution: 2.03→23.2 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.915 / SU B: 4.897 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.244 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23932 2295 5 %RANDOM
Rwork0.19079 ---
all0.1962 43165 --
obs0.19328 43165 97.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.599 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20.01 Å2
2---0.06 Å2-0 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.03→23.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6414 0 0 68 6482
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0196594
X-RAY DIFFRACTIONr_bond_other_d0.0020.026020
X-RAY DIFFRACTIONr_angle_refined_deg1.8491.9268990
X-RAY DIFFRACTIONr_angle_other_deg0.979313781
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7155822
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.76123.193332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.56615949
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9271556
X-RAY DIFFRACTIONr_chiral_restr0.130.2942
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217701
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021651
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.03→2.083 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 169 -
Rwork0.235 3071 -
obs--95.27 %

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