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- PDB-5bn7: Crystal structure of maltodextrin glucosidase from E.coli at 3.7 ... -

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Basic information

Entry
Database: PDB / ID: 5bn7
TitleCrystal structure of maltodextrin glucosidase from E.coli at 3.7 A resolution
ComponentsMaltodextrin glucosidase
KeywordsHYDROLASE / Glucosidase
Function / homology
Function and homology information


alpha-glucan catabolic process / alpha-1,4-glucosidase activity / maltose alpha-glucosidase activity / alpha-glucosidase / protein homodimerization activity / cytoplasm
Similarity search - Function
Maltodextrin glucosidase / Glycoside hydrolase, family 13, N-terminal Ig-like domain / Alpha amylase, N-terminal ig-like domain / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosyl hydrolase, all-beta / Glycosidases / Immunoglobulin E-set / Glycoside hydrolase superfamily ...Maltodextrin glucosidase / Glycoside hydrolase, family 13, N-terminal Ig-like domain / Alpha amylase, N-terminal ig-like domain / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosyl hydrolase, all-beta / Glycosidases / Immunoglobulin E-set / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Maltodextrin glucosidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsShukla, P.K. / Pastor, A. / Singh, A.K. / Sharma, S. / Singh, T.P. / Chaudhuri, T.K.
CitationJournal: Biochim.Biophys.Acta / Year: 2016
Title: Role of N-terminal region of Escherichia coli maltodextrin glucosidase in folding and function of the protein
Authors: Pastor, A. / Singh, A.K. / Shukla, P.K. / Equbal, M.J. / Malik, S.T. / Singh, T.P. / Chaudhuri, T.K.
History
DepositionMay 25, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2016Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maltodextrin glucosidase


Theoretical massNumber of molelcules
Total (without water)70,5271
Polymers70,5271
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area23490 Å2
Unit cell
Length a, b, c (Å)110.590, 110.590, 69.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4

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Components

#1: Protein Maltodextrin glucosidase / Alpha-glucosidase


Mass: 70527.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: malZ, b0403, JW0393 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P21517, alpha-glucosidase

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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: 3.01 Å3/Da / Density % sol: 59.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 2.5 M ammonium acetate, 0.1 M sodium acetate

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97625 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 18, 2014
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.525
11K, H, -L20.475
ReflectionResolution: 3.7→110.61 Å / Num. obs: 6156 / % possible obs: 70.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 88 Å2 / Rsym value: 0.097 / Net I/σ(I): 2.5
Reflection shellResolution: 3.7→3.79 Å / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 0.12 / % possible all: 73.9

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
iMOSFLMdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JI1

1ji1


Resolution: 3.7→110.61 Å / Cor.coef. Fo:Fc: 0.861 / Cor.coef. Fo:Fc free: 0.845 / Cross valid method: THROUGHOUT / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.34402 300 4.6 %RANDOM
Rwork0.32975 ---
obs0.3304 6156 70.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 131.048 Å2
Baniso -1Baniso -2Baniso -3
1-5.04 Å20 Å20 Å2
2--5.04 Å20 Å2
3----10.08 Å2
Refinement stepCycle: LAST / Resolution: 3.7→110.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3618 0 0 0 3618
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.023720
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.4251.9275059
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.0015450
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.12923.756197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.3115570
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8831527
X-RAY DIFFRACTIONr_chiral_restr0.1550.2522
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0212952
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.698→3.794 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.443 20 -
Rwork0.333 462 -
obs--70.47 %

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