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- PDB-5oss: Beta-glucosidase from Thermotoga maritima in complex with Gluco-1... -

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Basic information

Entry
Database: PDB / ID: 5oss
TitleBeta-glucosidase from Thermotoga maritima in complex with Gluco-1H-imidazole
ComponentsBeta-glucosidase A
KeywordsHYDROLASE / glycosylhydrolase / Thermotoga maritima / glucoimidazole
Function / homology
Function and homology information


: / beta-glucosidase / beta-glucosidase activity / cellulose catabolic process / cytosol
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
Chem-AEZ / Beta-glucosidase A
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsOffen, W.A. / Schroeder, S.P. / Davies, G.J. / Overkleeft, H.S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Research CouncilERC-2012-AdG-322942 United Kingdom
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: Gluco-1 H-imidazole: A New Class of Azole-Type beta-Glucosidase Inhibitor.
Authors: Schroder, S.P. / Wu, L. / Artola, M. / Hansen, T. / Offen, W.A. / Ferraz, M.J. / Li, K.Y. / Aerts, J.M.F.G. / van der Marel, G.A. / Codee, J.D.C. / Davies, G.J. / Overkleeft, H.S.
History
DepositionAug 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _citation.journal_volume ..._chem_comp.name / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.2May 9, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.3Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)108,76115
Polymers107,8812
Non-polymers87913
Water6,612367
1
A: Beta-glucosidase A
hetero molecules

B: Beta-glucosidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,76115
Polymers107,8812
Non-polymers87913
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x+1/2,-y-1/2,-z1
Buried area4450 Å2
ΔGint-9 kcal/mol
Surface area29660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.316, 94.616, 113.443
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 , 1 types, 2 molecules AB

#1: Protein Beta-glucosidase A / Beta-D-glucoside glucohydrolase / Cellobiase / Gentiobiase


Mass: 53940.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: bglA / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q08638, beta-glucosidase

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Non-polymers , 5 types, 380 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-AEZ / (4~{S},5~{S},6~{R},7~{R})-7-(hydroxymethyl)-4,5,6,7-tetrahydro-1~{H}-benzimidazole-4,5,6-triol


Mass: 200.192 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H12N2O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 367 / 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: 2.47 Å3/Da / Density % sol: 50.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: PEG 4000, imidazole, calcium acetate, trimethylamine oxide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97624 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 1.7→72.77 Å / Num. obs: 112065 / % possible obs: 100 % / Redundancy: 12.6 % / Net I/σ(I): 13.8
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 12.9 % / Rmerge(I) obs: 2.812 / Num. unique obs: 5461 / CC1/2: 0.61 / Rpim(I) all: 0.831 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
DIALSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OD0.PDB

1od0


Resolution: 1.7→72.77 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.499 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THERE IS UNMODELLED DENSITY NEAR HIS180A AND TWO ETHYLENE GLYCOL MOLECULES HAVE BEEN MODELLED AT PARTIAL OCCUPANCY BETWEEN GLU351A AND GLU405A.
RfactorNum. reflection% reflectionSelection details
Rfree0.22157 5629 5 %RANDOM
Rwork0.18628 ---
obs0.18804 106255 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.313 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å2-0 Å20 Å2
2--0.12 Å2-0 Å2
3---0.04 Å2
Refinement stepCycle: 1 / Resolution: 1.7→72.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7124 0 56 367 7547
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0197516
X-RAY DIFFRACTIONr_bond_other_d0.0020.026676
X-RAY DIFFRACTIONr_angle_refined_deg1.7721.92710226
X-RAY DIFFRACTIONr_angle_other_deg1.043315383
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3285906
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.14623.368380
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.379151130
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2411548
X-RAY DIFFRACTIONr_chiral_restr0.120.21045
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0218523
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021742
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_it3.1953.6253591
X-RAY DIFFRACTIONr_mcbond_other3.1943.6243590
X-RAY DIFFRACTIONr_mcangle_it3.9745.4254502
X-RAY DIFFRACTIONr_mcangle_other3.9735.4264503
X-RAY DIFFRACTIONr_scbond_it3.4583.7843925
X-RAY DIFFRACTIONr_scbond_other3.4573.7843926
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7125.5895723
X-RAY DIFFRACTIONr_long_range_B_refined5.81241.7368785
X-RAY DIFFRACTIONr_long_range_B_other5.81241.7358786
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 414 -
Rwork0.286 7754 -
obs--99.67 %

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