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- PDB-4aie: Structure of glucan-1,6-alpha-glucosidase from Lactobacillus acid... -

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Basic information

Entry
Database: PDB / ID: 4aie
TitleStructure of glucan-1,6-alpha-glucosidase from Lactobacillus acidophilus NCFM
ComponentsGLUCAN 1,6-ALPHA-GLUCOSIDASE
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE 13
Function / homology
Function and homology information


glucan 1,6-alpha-glucosidase / glucan 1,6-alpha-glucosidase activity / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Maltogenic Amylase, C-terminal / Maltogenic Amylase, C-terminal domain / Oligo-1,6-glucosidase; domain 2 / Oligo-1,6-glucosidase; Domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases ...Maltogenic Amylase, C-terminal / Maltogenic Amylase, C-terminal domain / Oligo-1,6-glucosidase; domain 2 / Oligo-1,6-glucosidase; Domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Glucan 1,6-alpha-glucosidase
Similarity search - Component
Biological speciesLACTOBACILLUS ACIDOPHILUS NCFM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsFredslund, F. / Navarro Poulsen, J.C. / Lo Leggio, L.
CitationJournal: J.Bacteriol. / Year: 2012
Title: Enzymology and Structure of the Gh13_31 Glucan 1,6-Alpha-Glucosidase that Confers Isomaltooligosaccharide Utilization in the Probiotic Lactobacillus Acidophilus Ncfm.
Authors: Moller, M.S. / Fredslund, F. / Majumder, A. / Nakai, H. / Poulsen, J.N. / Lo Leggio, L. / Svensson, B. / Abou Hachem, M.
History
DepositionFeb 9, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLUCAN 1,6-ALPHA-GLUCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,67113
Polymers64,3091
Non-polymers1,36312
Water8,557475
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.830, 107.250, 103.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2103-

HOH

21A-2123-

HOH

31A-2260-

HOH

41A-2323-

HOH

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Components

#1: Protein GLUCAN 1,6-ALPHA-GLUCOSIDASE / ALPHA-GLUCOSIDASE


Mass: 64308.633 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-539
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LACTOBACILLUS ACIDOPHILUS NCFM (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q5FMB7, glucan 1,6-alpha-glucosidase, oligo-1,6-glucosidase
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 475 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsSULFONIC MOIETY (MES A 1547): MODELLED AS PART OF MES MOLECULE

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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: 2.65 Å3/Da / Density % sol: 53.6 % / Description: NONE
Crystal growDetails: 20% GLYCEROL, 16% PEG 8K, 0.1 M MES PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.03796
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 16, 2009 / Details: MIRRORS
RadiationMonochromator: BENT SI (111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03796 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. obs: 39496 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 16.68 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 25.5
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 9.7 / % possible all: 91.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZIC

2zic


Resolution: 2.05→29.424 Å / SU ML: 0.22 / σ(F): 1.99 / Phase error: 15.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1834 1997 5.1 %
Rwork0.1371 --
obs0.1395 39494 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.878 Å2 / ksol: 0.393 e/Å3
Displacement parametersBiso mean: 17.4 Å2
Baniso -1Baniso -2Baniso -3
1--3.7132 Å20 Å20 Å2
2--5.269 Å20 Å2
3----1.5558 Å2
Refinement stepCycle: LAST / Resolution: 2.05→29.424 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4426 0 77 475 4978
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014616
X-RAY DIFFRACTIONf_angle_d1.2376251
X-RAY DIFFRACTIONf_dihedral_angle_d14.561723
X-RAY DIFFRACTIONf_chiral_restr0.078633
X-RAY DIFFRACTIONf_plane_restr0.006815
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.10120.22091410.18582572X-RAY DIFFRACTION98
2.1012-2.1580.20371370.13822683X-RAY DIFFRACTION100
2.158-2.22150.20441470.12622652X-RAY DIFFRACTION100
2.2215-2.29320.20991350.13752588X-RAY DIFFRACTION98
2.2932-2.37510.20441460.12582675X-RAY DIFFRACTION100
2.3751-2.47020.17831350.11572663X-RAY DIFFRACTION100
2.4702-2.58250.18181450.11822686X-RAY DIFFRACTION100
2.5825-2.71860.18361420.12362669X-RAY DIFFRACTION100
2.7186-2.88880.17841480.12192674X-RAY DIFFRACTION100
2.8888-3.11160.17631470.12482712X-RAY DIFFRACTION100
3.1116-3.42430.1811390.13372685X-RAY DIFFRACTION100
3.4243-3.91880.15181430.13822688X-RAY DIFFRACTION98
3.9188-4.93350.151420.12362722X-RAY DIFFRACTION99
4.9335-29.42690.2261500.19592828X-RAY DIFFRACTION97

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