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- PDB-5xgz: Metagenomic glucose-tolerant glycosidase -

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Basic information

Entry
Database: PDB / ID: 5xgz
TitleMetagenomic glucose-tolerant glycosidase
ComponentsBeta-glycosidase
KeywordsHYDROLASE / beta-glycosidase / meta genome / thermostable enzyme / glucose-tolerant
Function / homology
Function and homology information


beta-glucosidase / beta-glucosidase activity / cellulose catabolic process
Similarity search - Function
Glycoside hydrolase, family 1, beta-glucosidase / Glycoside hydrolase family 1, active site / Glycosyl hydrolases family 1 active site. / Glycosyl hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel ...Glycoside hydrolase, family 1, beta-glucosidase / Glycoside hydrolase family 1, active site / Glycosyl hydrolases family 1 active site. / Glycosyl hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / beta-glucosidase
Similarity search - Component
Biological speciesuncultured microorganism (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsWatanabe, M. / Matsuzawa, T. / Yaoi, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
JSPS26850067 Japan
Citation
Journal: Appl.Microbiol.Biotechnol. / Year: 2017
Title: Improved thermostability of a metagenomic glucose-tolerant beta-glycosidase based on its X-ray crystal structure.
Authors: Matsuzawa, T. / Watanabe, M. / Yaoi, K.
#1: Journal: To Be Published
Title: Metagenomic glucose-tolerant glycosidase
Authors: Watanabe, M. / Matsuzawa, T. / Yaoi, K.
History
DepositionApr 19, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Nov 22, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)105,98023
Polymers104,1722
Non-polymers1,80821
Water9,188510
1
A: Beta-glycosidase
B: Beta-glycosidase
hetero molecules

A: Beta-glycosidase
B: Beta-glycosidase
hetero molecules

A: Beta-glycosidase
B: Beta-glycosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)317,94069
Polymers312,5156
Non-polymers5,42563
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation12_555-y,-z,x1
Buried area10960 Å2
ΔGint-86 kcal/mol
Surface area92540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)202.427, 202.427, 202.427
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein Beta-glycosidase


Mass: 52085.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured microorganism (environmental samples)
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1E1FFN6
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 510 / 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: 3.31 Å3/Da / Density % sol: 62.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris-HCl buffer, 1.3 M lithium sulfate, 0.01 M nickel chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 134784 / % possible obs: 98 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.027 / Rrim(I) all: 0.095 / Χ2: 1.451 / Net I/σ(I): 9.5 / Num. measured all: 1151056
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsRpim(I) allRrim(I) allΧ2% possible allCC1/2
1.75-1.783.20.40163600.2430.4730.72893.3
1.78-1.813.30.39364820.2340.4610.72994.20.035
1.81-1.853.40.38965210.2260.4530.76995.20.028
1.85-1.893.60.38565300.2150.4440.80995.40.081
1.89-1.933.70.37665710.2050.4310.83396.10.105
1.93-1.974.10.36165850.1870.410.88496.70.231
1.97-2.024.40.35166970.1740.3950.9297.20.304
2.02-2.074.80.33866900.1580.3760.99298.10.46
2.07-2.145.40.32167630.1420.3531.06498.40.597
2.14-2.25.90.30767480.1290.3351.0998.60.698
2.2-2.286.70.27867780.1070.2991.299.10.84
2.28-2.387.50.25767890.0930.2741.23399.10.897
2.38-2.488.50.22668720.0760.241.25599.50.936
2.48-2.619.70.19668250.0620.2061.27799.50.968
2.61-2.7810.80.16568340.0490.1731.31599.50.983
2.78-2.9912.20.14769010.040.1531.59499.70.99
2.99-3.2914.20.12368610.0310.1272.29499.80.996
3.29-3.77170.07769470.0180.0791.95899.90.998
3.77-4.7519.60.04969260.0110.051.55299.90.999
4.75-5020.40.04271040.0090.0431.48799.81

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JIE

2jie


Resolution: 1.75→30 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.925 / SU B: 8.499 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25477 6676 5 %RANDOM
Rwork0.20633 ---
obs0.20875 128017 97.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.865 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.75→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7206 0 104 510 7820
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0197592
X-RAY DIFFRACTIONr_bond_other_d0.0020.026674
X-RAY DIFFRACTIONr_angle_refined_deg1.841.93410344
X-RAY DIFFRACTIONr_angle_other_deg1.128315395
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.845902
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.81522.988405
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.544151095
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9871568
X-RAY DIFFRACTIONr_chiral_restr0.1290.21050
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0218608
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021764
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_it2.9091.8773587
X-RAY DIFFRACTIONr_mcbond_other2.8921.8753586
X-RAY DIFFRACTIONr_mcangle_it3.4552.8084490
X-RAY DIFFRACTIONr_mcangle_other3.4592.814491
X-RAY DIFFRACTIONr_scbond_it4.4692.2184005
X-RAY DIFFRACTIONr_scbond_other4.4362.2183997
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1133.1945841
X-RAY DIFFRACTIONr_long_range_B_refined4.65836.32334124
X-RAY DIFFRACTIONr_long_range_B_other4.59936.22733821
X-RAY DIFFRACTIONr_rigid_bond_restr4.285314266
X-RAY DIFFRACTIONr_sphericity_free26.9315161
X-RAY DIFFRACTIONr_sphericity_bonded10.097514397
LS refinement shellResolution: 1.751→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.461 447 -
Rwork0.452 8957 -
obs--93.48 %

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