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- PDB-2g3n: Crystal structure of the Sulfolobus solfataricus alpha-glucosidas... -

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Basic information

Entry
Database: PDB / ID: 2g3n
TitleCrystal structure of the Sulfolobus solfataricus alpha-glucosidase MalA in complex with beta-octyl-glucopyranoside
ComponentsAlpha-glucosidase
KeywordsHYDROLASE / alpha-glucosidase / enzyme-carbohydrate complex / glycoside hydrolase family 31 / multidomain protein / (beta/alpha)8 barrel / retaining mechanism
Function / homology
Function and homology information


alpha-glucosidase / maltose alpha-glucosidase activity / N-glycan processing / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / cytoplasm
Similarity search - Function
glycosyl hydrolase (family 31) / Glycosyl hydrolases family 31, active site / Glycosyl hydrolases family 31 active site. / Glycoside hydrolase family 31, N-terminal domain / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain / : / Glycosyl hydrolase family 31 C-terminal domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / Galactose mutarotase-like domain superfamily ...glycosyl hydrolase (family 31) / Glycosyl hydrolases family 31, active site / Glycosyl hydrolases family 31 active site. / Glycoside hydrolase family 31, N-terminal domain / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain / : / Glycosyl hydrolase family 31 C-terminal domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / Galactose mutarotase-like domain superfamily / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Alpha-glucosidase / Alpha-glucosidase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsErnst, H.A. / Lo Leggio, L. / Willemoes, M. / Leonard, G. / Blum, P. / Larsen, S.
Citation
Journal: J.Mol.Biol. / Year: 2006
Title: Structure of the Sulfolobus solfataricus alpha-Glucosidase: Implications for Domain Conservation and Substrate Recognition in GH31.
Authors: Ernst, H.A. / Lo Leggio, L. / Willemoes, M. / Leonard, G. / Blum, P. / Larsen, S.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Characterization of different crystal forms of the alpha-glucosidase MalA from Sulfolobus solfataricus
Authors: Ernst, H.A. / Willemoes, M. / Lo Leggio, L. / Leonard, G. / Blum, P. / Larsen, S.
History
DepositionFeb 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 30, 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: Alpha-glucosidase
B: Alpha-glucosidase
C: Alpha-glucosidase
D: Alpha-glucosidase
E: Alpha-glucosidase
F: Alpha-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)485,23512
Polymers483,4816
Non-polymers1,7546
Water11,079615
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26590 Å2
ΔGint-84 kcal/mol
Surface area131740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.090, 174.430, 144.030
Angle α, β, γ (deg.)90.00, 109.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Alpha-glucosidase / / Maltase


Mass: 80580.195 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: 98-2 / Gene: malA / Plasmid: pMW800 / Production host: Escherichia coli (E. coli) / Strain (production host): NF1830
References: UniProt: O59645, UniProt: P0CD66*PLUS, alpha-glucosidase
#2: Sugar
ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 615 / 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: 2.46 Å3/Da / Density % sol: 49.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 10 % PEG 4000, 0.2 M sodium citrate, 0.1 M sodium acetate, 0.5 % beta-octyl-glucopyranoside, microseeding, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 27, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.5→24.2 Å / Num. obs: 154885 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 34.5 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 11.67
Reflection shellResolution: 2.5→2.63 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 5.3

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Phasing

Phasing MRRfactor: 0.391 / Cor.coef. Fo:Fc: 0.643
Highest resolutionLowest resolution
Rotation2.5 Å24.16 Å
Translation2.5 Å24.16 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
CNS1.1refinement
PDB_EXTRACT1.701data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: A trimmed version of the trimer in PDB code 2G3M

2g3m


Resolution: 2.55→24.16 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 3189066.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: maximum likelihood
RfactorNum. reflection% reflectionSelection details
Rfree0.213 7300 5 %RANDOM
Rwork0.191 ---
obs0.191 145907 96.3 %-
all-154885 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.366 Å2 / ksol: 0.382443 e/Å3
Displacement parametersBiso mean: 43.2 Å2
Baniso -1Baniso -2Baniso -3
1-16.62 Å20 Å27.9 Å2
2---5.3 Å20 Å2
3----11.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.55→24.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34098 0 84 615 34797
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.21.5
X-RAY DIFFRACTIONc_mcangle_it22
X-RAY DIFFRACTIONc_scbond_it1.962
X-RAY DIFFRACTIONc_scangle_it3.072.5
Refine LS restraints NCSNCS model details: RESTRAINED
LS refinement shellResolution: 2.55→2.71 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.301 1228 4.9 %
Rwork0.265 23650 -
obs--98.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein_nohydrogen.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3cis_peptide.paramBOG_trunc.top
X-RAY DIFFRACTION4BOG_trunc.param

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