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- PDB-5n6t: Thermotoga maritima family 1 glycoside hydrolase complexed with a... -

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Basic information

Entry
Database: PDB / ID: 5n6t
TitleThermotoga maritima family 1 glycoside hydrolase complexed with a cyclophellitol analogue transition state mimic
ComponentsBeta-glucosidase A
KeywordsHYDROLASE / carba-cyclophellitol / mimic
Function / homology
Function and homology information


scopolin beta-glucosidase activity / 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-8P2 / Beta-glucosidase A
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsOffen, W. / Davies, G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Research CouncilERC-2012-AdG-322942 United Kingdom
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: Carba-cyclophellitols Are Neutral Retaining-Glucosidase Inhibitors.
Authors: Beenakker, T.J.M. / Wander, D.P.A. / Offen, W.A. / Artola, M. / Raich, L. / Ferraz, M.J. / Li, K.Y. / Houben, J.H.P.M. / van Rijssel, E.R. / Hansen, T. / van der Marel, G.A. / Codee, J.D.C. ...Authors: Beenakker, T.J.M. / Wander, D.P.A. / Offen, W.A. / Artola, M. / Raich, L. / Ferraz, M.J. / Li, K.Y. / Houben, J.H.P.M. / van Rijssel, E.R. / Hansen, T. / van der Marel, G.A. / Codee, J.D.C. / Aerts, J.M.F.G. / Rovira, C. / Davies, G.J. / Overkleeft, H.S.
History
DepositionFeb 16, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references
Revision 1.2May 24, 2017Group: Database references
Revision 1.3Feb 20, 2019Group: Author supporting evidence / Data collection / Derived calculations
Category: pdbx_audit_support / pdbx_data_processing_status ...pdbx_audit_support / pdbx_data_processing_status / struct_conn / struct_conn_type
Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 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)108,66411
Polymers107,8812
Non-polymers7829
Water4,720262
1
A: Beta-glucosidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3496
Polymers53,9411
Non-polymers4095
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-glucosidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3145
Polymers53,9411
Non-polymers3734
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.839, 94.840, 112.930
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 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 (bacteria) / Gene: bglA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q08638, beta-glucosidase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-8P2 / [(1~{R},2~{R},3~{R},4~{S},5~{R},6~{S})-3,4,5-tris(oxidanyl)-7-oxabicyclo[4.1.0]heptan-2-yl]methanediazonium


Mass: 187.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H11N2O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.8 Å3/Da / Density % sol: 55.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: PEG 4000, potassium sodium tartrate, bis-tris propane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.1→56.46 Å / Num. obs: 60171 / % possible obs: 100 % / Redundancy: 7.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.044 / Net I/σ(I): 12.8
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.966 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4395 / CC1/2: 0.623 / Rpim(I) all: 0.408 / % possible all: 100

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Processing

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

1od0


Resolution: 2.1→56.41 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.932 / SU B: 5.78 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.207 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23666 3042 5.1 %RANDOM
Rwork0.18396 ---
obs0.18671 57056 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.576 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å2-0 Å20 Å2
2--0.71 Å2-0 Å2
3----0.13 Å2
Refinement stepCycle: 1 / Resolution: 2.1→56.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7108 0 49 262 7419
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0197452
X-RAY DIFFRACTIONr_bond_other_d0.0020.026545
X-RAY DIFFRACTIONr_angle_refined_deg1.7291.92610147
X-RAY DIFFRACTIONr_angle_other_deg1.069315075
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8925897
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.38623.439378
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.704151097
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7421546
X-RAY DIFFRACTIONr_chiral_restr0.1040.21043
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218457
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021725
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_it3.0243.6583579
X-RAY DIFFRACTIONr_mcbond_other3.0243.6573578
X-RAY DIFFRACTIONr_mcangle_it4.3055.4764480
X-RAY DIFFRACTIONr_mcangle_other4.3055.4774481
X-RAY DIFFRACTIONr_scbond_it3.0843.6963873
X-RAY DIFFRACTIONr_scbond_other3.093.6953874
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4515.4865662
X-RAY DIFFRACTIONr_long_range_B_refined5.99841.3268667
X-RAY DIFFRACTIONr_long_range_B_other5.99841.3258667
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 221 -
Rwork0.279 4161 -
obs--100 %

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