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- PDB-4mdo: Crystal structure of a GH1 beta-glucosidase from the fungus Humic... -

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Basic information

Entry
Database: PDB / ID: 4mdo
TitleCrystal structure of a GH1 beta-glucosidase from the fungus Humicola insolens
ComponentsBeta-glucosidase
KeywordsHYDROLASE / Glycoside Hydrolase Family 1 / TIM barrel / retaining enzyme
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
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
DI(HYDROXYETHYL)ETHER / Beta-glucosidase
Similarity search - Component
Biological speciesHumicola grisea var. thermoidea (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGiuseppe, P.O. / Souza, T.A.C.B. / Souza, F.H.M. / Zanphorlin, L.M. / Machado, C.B. / Ward, R.J. / Jorge, J.A. / Furriel, R.P.M. / Murakami, M.T.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structural basis for glucose tolerance in GH1 beta-glucosidases.
Authors: Giuseppe, P.O. / Souza, T.A.C.B. / Souza, F.H.M. / Zanphorlin, L.M. / Machado, C.B. / Ward, R.J. / Jorge, J.A. / Furriel, R.P.M. / Murakami, M.T.
History
DepositionAug 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9124
Polymers56,5871
Non-polymers3243
Water3,855214
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)113.543, 113.543, 179.058
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Beta-glucosidase


Mass: 56587.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Humicola grisea var. thermoidea (fungus)
Gene: bgl4 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O93784
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.94 Å3/Da / Density % sol: 58.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 2 M lithium sulfate, 2%PEG 400, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.459 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 21446 / % possible obs: 98.7 %
Reflection shellResolution: 2.6→2.69 Å / % possible all: 98.6

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→28.95 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.901 / WRfactor Rfree: 0.2128 / WRfactor Rwork: 0.1523 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8525 / SU B: 8.76 / SU ML: 0.184 / SU R Cruickshank DPI: 0.457 / SU Rfree: 0.2833 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.457 / ESU R Free: 0.283 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1088 5.1 %RANDOM
Rwork0.1683 ---
obs0.1717 21267 97.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.92 Å2 / Biso mean: 30.1458 Å2 / Biso min: 9.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.02 Å20 Å2
2--0.02 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.6→28.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3833 0 20 214 4067
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193967
X-RAY DIFFRACTIONr_bond_other_d0.0010.023606
X-RAY DIFFRACTIONr_angle_refined_deg1.421.9485381
X-RAY DIFFRACTIONr_angle_other_deg0.79638324
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0855476
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.53623.838198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.9715625
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8591523
X-RAY DIFFRACTIONr_chiral_restr0.0760.2541
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214520
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02957
X-RAY DIFFRACTIONr_mcbond_it1.5972.9241908
X-RAY DIFFRACTIONr_mcbond_other1.5942.9231906
X-RAY DIFFRACTIONr_mcangle_it2.564.382382
LS refinement shellResolution: 2.598→2.665 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 72 -
Rwork0.258 1441 -
all-1513 -
obs--97.74 %

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