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- PDB-5ayi: Crystal structure of GH1 Beta-glucosidase TD2F2 N223Q mutant -

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Basic information

Entry
Database: PDB / ID: 5ayi
TitleCrystal structure of GH1 Beta-glucosidase TD2F2 N223Q mutant
ComponentsBETA-GLUCOSIDASE
KeywordsHYDROLASE / TIM BARREL
Function / homologyGlycosidases / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / beta-D-glucopyranose
Function and homology information
Biological speciesmetagenomes (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 21, 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: chem_comp / diffrn_source / pdbx_struct_oper_list
Item: _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4566
Polymers50,8611
Non-polymers5955
Water6,810378
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-6 kcal/mol
Surface area15870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.060, 69.803, 96.335
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein BETA-GLUCOSIDASE /


Mass: 50860.883 Da / Num. of mol.: 1 / Mutation: N223Q
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
#4: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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

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Non-polymers , 4 types, 382 molecules

#2: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES / CHES (buffer)


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
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 378 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. RESIDUE 223 GLN REPRESENT ...A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. RESIDUE 223 GLN REPRESENT MUTATION N223Q.

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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, hanging 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: Nov 8, 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: 1.85→50 Å / Num. obs: 40537 / % possible obs: 100 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.131 / Net I/σ(I): 13.4
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 3.3 / % 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: 1.85→45.97 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.411 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17543 2030 5 %RANDOM
Rwork0.13995 ---
obs0.14173 38446 99.94 %-
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: 13.71 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.85→45.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3470 0 38 378 3886
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193615
X-RAY DIFFRACTIONr_bond_other_d0.0060.023299
X-RAY DIFFRACTIONr_angle_refined_deg1.8471.954930
X-RAY DIFFRACTIONr_angle_other_deg1.09137556
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6375442
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.13323.132182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.10115514
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4691530
X-RAY DIFFRACTIONr_chiral_restr0.1310.2515
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214166
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02896
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_it1.3291.2011765
X-RAY DIFFRACTIONr_mcbond_other1.3291.1991764
X-RAY DIFFRACTIONr_mcangle_it1.9461.7922205
X-RAY DIFFRACTIONr_mcangle_other1.9451.7942206
X-RAY DIFFRACTIONr_scbond_it2.0531.3961850
X-RAY DIFFRACTIONr_scbond_other2.0511.3961850
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1592.0232725
X-RAY DIFFRACTIONr_long_range_B_refined4.96910.6414533
X-RAY DIFFRACTIONr_long_range_B_other4.96910.6424533
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.849→1.897 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 140 -
Rwork0.173 2781 -
obs--99.56 %

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