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- PDB-3poc: The crystal structure of the D307A mutant of alpha-Glucosidase (F... -

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Basic information

Entry
Database: PDB / ID: 3poc
TitleThe crystal structure of the D307A mutant of alpha-Glucosidase (FAMILY 31) from Ruminococcus obeum ATCC 29174 in complex with acarbose
Componentsalpha-Glucosidase
Keywordshydrolase/hydrolase inhibitor / structural genomics / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG / multi-domain / alpha-Glucosidase / cytoplasmic / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
Immunoglobulin-like - #4040 / 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 ...Immunoglobulin-like - #4040 / 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 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
alpha-acarbose / Chem-AC1 / alpha-D-glucopyranose / Glycosyl hydrolase, family 31
Similarity search - Component
Biological speciesRuminococcus obeum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsTan, K. / Tesar, C. / Wilton, R. / Keigher, L. / Babnigg, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the D307A mutant of alpha-Glucosidase (FAMILY 31) from Ruminococcus obeum ATCC 29174 in complex with acarbose
Authors: Tan, K. / Tesar, C. / Wilton, R. / Keigher, L. / Babnigg, G. / Joachimiak, A.
History
DepositionNov 22, 2010Deposition site: RCSB / Processing site: RCSB
SupersessionJan 26, 2011ID: 3NQQ
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.pdbx_PDB_ins_code / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_PDB_ins_code / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_ins_code / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_assembly_gen.asym_id_list / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 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

Downloads & links

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Assembly

Deposited unit
A: alpha-Glucosidase
B: alpha-Glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,3717
Polymers154,8112
Non-polymers1,5615
Water9,296516
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6770 Å2
ΔGint-30 kcal/mol
Surface area44570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.954, 125.691, 87.968
Angle α, β, γ (deg.)90.00, 107.62, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe chains A and B form a dimer.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein alpha-Glucosidase


Mass: 77405.453 Da / Num. of mol.: 2 / Mutation: D307A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus obeum (bacteria) / Strain: ATCC 29174 / Gene: RUMOBE_03919 / Plasmid: PMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): PPK1037 / References: UniProt: A5ZY13

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Sugars , 3 types, 4 molecules

#2: Polysaccharide 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D- ...4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-acarbose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 645.606 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-acarbose
DescriptorTypeProgram
WURCS=2.0/2,3,2/[a2122h-1a_1-5][a2122m-1a_1-5_4*NC^SC^SC^SC^RCCO/7=^ZC$3/6O/5O/4O]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-6-deoxy-Glcp4N]{[(4+1)][<C7O4>]{}}}}LINUCSPDB-CARE
#3: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Sugar ChemComp-AC1 / 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose / 6-METHYL-5-(4,5,6-TRIHYDROXY-3-HYDROXYMETHYL-CYCLOHEX-2-ENYLAMINO)-TETRAHYDRO-PYRAN-2,3,4-TRIOL / 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucose / 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-D-glucose / 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-glucose


Type: D-saccharide / Mass: 321.324 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C13H23NO8

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Non-polymers , 2 types, 517 molecules

#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 516 / 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: 2.31 Å3/Da / Density % sol: 46.82 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M BIS-TRIS, 25% PEG3350, 10% ACARBOSE, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 22, 2010 / Details: MIRROR
RadiationMonochromator: SI 111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 1.99→42 Å / Num. all: 91803 / Num. obs: 91803 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 12.2
Reflection shellResolution: 2→2.03 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.585 / Mean I/σ(I) obs: 1.16 / % possible all: 84.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3N04

3n04


Resolution: 1.99→41.365 Å / SU ML: 0.27 / σ(F): 0 / Phase error: 28.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2246 4097 5.06 %
Rwork0.1676 --
obs0.1705 80967 84.07 %
all-80668 -
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.417 Å2 / ksol: 0.321 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-22.3608 Å2-0 Å24.9589 Å2
2---8.6732 Å20 Å2
3----13.6876 Å2
Refinement stepCycle: LAST / Resolution: 1.99→41.365 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10866 0 86 516 11468
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711274
X-RAY DIFFRACTIONf_angle_d1.02815218
X-RAY DIFFRACTIONf_dihedral_angle_d14.8354306
X-RAY DIFFRACTIONf_chiral_restr0.0741514
X-RAY DIFFRACTIONf_plane_restr0.0041981
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9898-2.06090.34133110.28795523X-RAY DIFFRACTION61
2.0609-2.14340.33133520.25896324X-RAY DIFFRACTION70
2.1434-2.24090.2853550.22286734X-RAY DIFFRACTION74
2.2409-2.35910.27823530.2067122X-RAY DIFFRACTION78
2.3591-2.50680.28014180.19617647X-RAY DIFFRACTION84
2.5068-2.70040.26164090.19358048X-RAY DIFFRACTION88
2.7004-2.9720.27514660.18768398X-RAY DIFFRACTION92
2.972-3.40190.24234680.17178834X-RAY DIFFRACTION96
3.4019-4.28540.17674720.13419033X-RAY DIFFRACTION99
4.2854-41.37390.16164930.12589207X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2041-0.05760.04570.5667-0.30061.19880.024-0.0278-0.00810.07930.0304-0.0038-0.205-0.1456-0.05330.17060.03750.02370.16190.0090.1411-33.4412-2.610958.2488
20.4628-0.1079-0.14640.18590.04990.8015-0.06410.0583-0.0427-0.20520.05130.0152-0.1824-0.11570.01540.37860.03430.0060.14850.00170.1392-32.92571.839617.9506
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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