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- PDB-2g3m: Crystal structure of the Sulfolobus solfataricus alpha-glucosidas... -

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Basic information

Entry
Database: PDB / ID: 2g3m
TitleCrystal structure of the Sulfolobus solfataricus alpha-glucosidase MalA
ComponentsAlpha-glucosidase
KeywordsHYDROLASE / alpha-glucosidase / glycoside hydrolase family 31 / multidomain protein / (beta/alpha)8 barrel / retaining mechanism
Function / homology
Function and homology information


: / alpha-1,4-glucosidase activity / alpha-glucosidase / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process / 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 ...: / 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 1.3Aug 30, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)483,4816
Polymers483,4816
Non-polymers00
Water22,7531263
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24320 Å2
ΔGint-83 kcal/mol
Surface area132260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.170, 173.560, 154.080
Angle α, β, γ (deg.)90.00, 108.00, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1263 / 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: 2.71 Å3/Da / Density % sol: 54.65 %
Description: LOCKED ROTATION FUNCTION WITH NCS POINT GROUP 32
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.1
Details: 11% PEG 4000, 0.2 M sodium citrate, 0.1 M sodium acetate, microseeding, pH 4.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9791 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 20, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.55→35 Å / Num. all: 167412 / Num. obs: 167412 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 35.6 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 16.78
Reflection shellResolution: 2.55→2.65 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.304 / Mean I/σ(I) obs: 7.1

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Phasing

Phasing MRRfactor: 0.541 / Cor.coef. Fo:Fc: 0.279
Highest resolutionLowest resolution
Translation4.5 Å34.25 Å
Phasing dmFOM centric: 0.6 / Reflection centric: 3619
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.3-29.8060.880.880.7871956783412
4.6-7.30.850.850.742235421656698
3.6-4.60.860.870.782806427419645
3.2-3.60.770.770.672826127718543
2.7-3.20.540.540.445029049447843
2.6-2.70.30.30.233121530737478

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
RESOLVE2.08phasing
CNS1.1refinement
PDB_EXTRACT1.701data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Trimmed polyalanine version of PDB CODE 1XSI (A chain)

1xsi


Resolution: 2.55→34.25 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 5001250.51 / 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
Rfree0.195 8380 5 %RANDOM
Rwork0.17 ---
obs0.17 167412 99.9 %-
all-167412 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.7982 Å2 / ksol: 0.3586 e/Å3
Displacement parametersBiso mean: 34.8 Å2
Baniso -1Baniso -2Baniso -3
1-9.23 Å20 Å27.06 Å2
2---5.69 Å20 Å2
3----3.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.55→34.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34115 0 0 1263 35378
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_d24
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.141.5
X-RAY DIFFRACTIONc_mcangle_it1.892
X-RAY DIFFRACTIONc_scbond_it1.972
X-RAY DIFFRACTIONc_scangle_it3.012.5
Refine LS restraints NCSNCS model details: RESTRAINED
LS refinement shellResolution: 2.55→2.71 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.266 1354 4.9 %
Rwork0.222 26456 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein_nohydrogen.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3cis_peptide.param

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