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- PDB-5ayb: Crystal structure of GH1 Beta-Glucosidase TD2F2 N223G mutant -

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Basic information

Entry
Database: PDB / ID: 5ayb
TitleCrystal structure of GH1 Beta-Glucosidase TD2F2 N223G mutant
ComponentsBETA-GLUCOSIDASE
KeywordsHYDROLASE / TIM BARREL
Function / homologyGlycosidases / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Function and homology information
Biological speciesmetagenomes (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsJo, T. / Manninen, J.A. / Matsuzawa, T. / Uchiyama, T. / Yaoi, K. / Arakawa, T. / Fushinobu, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
New Energy and Industrial Technology Development Organization Japan
Citation
Journal: Febs J. / Year: 2016
Title: Crystal structure and identification of a key amino acid for glucose tolerance, substrate specificity, and transglycosylation activity of metagenomic beta-glucosidase Td2F2
Authors: Matsuzawa, T. / Jo, T. / Uchiyama, T. / Manninen, J.A. / Arakawa, T. / Miyazaki, K. / Fushinobu, S. / Yaoi, K.
#1: Journal: J. Biol. Chem. / Year: 2013
Title: Characterization of a novel beta-glucosidase from a compost microbial metagenome with strong transglycosylation activity.
Authors: Uchiyama, T. / Miyazaki, K. / Yaoi, K.
History
DepositionAug 12, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 1.2Jul 6, 2016Group: Database references
Revision 1.3Feb 26, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BETA-GLUCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1445
Polymers50,7901
Non-polymers3544
Water5,098283
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-5 kcal/mol
Surface area15880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.902, 69.839, 96.104
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein BETA-GLUCOSIDASE


Mass: 50789.805 Da / Num. of mol.: 1 / Mutation: N223G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenomes (others) / Plasmid: PJTTD2F2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: beta-glucosidase
#2: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. RESIDUE 223 GLY REPRESENT ...A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. RESIDUE 223 GLY REPRESENT MUTATION N223G.

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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: 2.28 Å3/Da / Density % sol: 45.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1.2M K/NA TARTRATE, 0.1M NA-CHES, 0.2M LI2SO4, PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 22, 2014
RadiationMonochromator: NUMERICAL LINK TYPE SI(111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 43580 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 14.3 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 20
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.702 / Mean I/σ(I) obs: 2.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WH5

3wh5


Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.96 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1643 2190 5 %RANDOM
Rwork0.13807 ---
obs0.13938 41327 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.934 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3454 0 22 283 3759
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0193583
X-RAY DIFFRACTIONr_bond_other_d0.0060.023271
X-RAY DIFFRACTIONr_angle_refined_deg1.7581.9464886
X-RAY DIFFRACTIONr_angle_other_deg1.06837490
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.25441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.10823.167180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.91215509
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4271529
X-RAY DIFFRACTIONr_chiral_restr0.1320.2506
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214148
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02889
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_it1.7381.7991761
X-RAY DIFFRACTIONr_mcbond_other1.7281.7971760
X-RAY DIFFRACTIONr_mcangle_it2.3422.6882200
X-RAY DIFFRACTIONr_mcangle_other2.3472.692201
X-RAY DIFFRACTIONr_scbond_it2.7662.0411822
X-RAY DIFFRACTIONr_scbond_other2.7622.0411822
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9252.9712686
X-RAY DIFFRACTIONr_long_range_B_refined5.21615.6174387
X-RAY DIFFRACTIONr_long_range_B_other5.07715.254263
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.802→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.207 159 -
Rwork0.18 2974 -
obs--98.12 %

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