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- PDB-6ca1: THE CRYSTAL STRUCTURE OF THE W169Y MUTANT OF ALPHA-GLUCOSIDASE (G... -

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Basic information

Entry
Database: PDB / ID: 6ca1
TitleTHE CRYSTAL STRUCTURE OF THE W169Y MUTANT OF ALPHA-GLUCOSIDASE (GH 31) FROM RUMINOCOCCUS OBEUM ATCC 29174 in complex with miglitol
ComponentsGlycosyl hydrolase, family 31
KeywordsHYDROLASE / structural genomics / PSI-Biology / protein structure initiative / midwest center for structural genomics / MCSG
Function / homology
Function and homology information


glucan 1,4-alpha-glucosidase / 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
Chem-MIG / Glucan 1,4-alpha-glucosidase
Similarity search - Component
Biological speciesBlautia obeum ATCC 29174 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsTan, K. / Tesar, C. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Macromolecular Research (MCMR) / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Protein Sci. / Year: 2018
Title: Interaction of antidiabetic alpha-glucosidase inhibitors and gut bacteria alpha-glucosidase.
Authors: Tan, K. / Tesar, C. / Wilton, R. / Jedrzejczak, R.P. / Joachimiak, A.
History
DepositionJan 29, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 21, 2021Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Sep 30, 2026Group: Database references / Other / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / pdbx_SG_project / pdbx_entry_details / struct_keywords
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_SG_project.full_name_of_center / _pdbx_SG_project.initial_of_center / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycosyl hydrolase, family 31
B: Glycosyl hydrolase, family 31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,4986
Polymers154,8992
Non-polymers5994
Water14,520806
1
A: Glycosyl hydrolase, family 31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,7493
Polymers77,4491
Non-polymers2992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycosyl hydrolase, family 31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,7493
Polymers77,4491
Non-polymers2992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6000 Å2
ΔGint-26 kcal/mol
Surface area44030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.749, 70.058, 88.162
Angle α, β, γ (deg.)111.32, 107.59, 97.67
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Glycosyl hydrolase, family 31


Mass: 77449.461 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Blautia obeum ATCC 29174 (bacteria) / Gene: RUMOBE_03919 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic
References: UniProt: A5ZY13, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Chemical ChemComp-MIG / (2R,3R,4R,5S)-1-(2-hydroxyethyl)-2-(hydroxymethyl)piperidine-3,4,5-triol / Miglitol


Mass: 207.224 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H17NO5 / Comment: inhibitor*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 806 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.2 Å3/Da / Density % sol: 44.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1M Bis-Tris, 25% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.95→32 Å / Num. obs: 93150 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Biso Wilson estimate: 20.85 Å2 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.075 / Rrim(I) all: 0.106 / Χ2: 1.017 / Net I/σ(I): 11.7
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4384 / CC1/2: 0.622 / Rpim(I) all: 0.424 / Rrim(I) all: 0.599 / Χ2: 0.783 / % possible all: 91.5

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3N04

3n04


Resolution: 1.95→31.545 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 22.22
RfactorNum. reflection% reflectionSelection details
Rfree0.2014 4668 5.01 %Random
Rwork0.1516 ---
obs0.1541 93102 96.32 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.95→31.545 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10833 0 40 806 11679
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611170
X-RAY DIFFRACTIONf_angle_d1.05115072
X-RAY DIFFRACTIONf_dihedral_angle_d14.2994150
X-RAY DIFFRACTIONf_chiral_restr0.0781520
X-RAY DIFFRACTIONf_plane_restr0.0051972
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9486-1.97070.29571170.22152619X-RAY DIFFRACTION85
1.9707-1.99390.25161260.20812804X-RAY DIFFRACTION91
1.9939-2.01820.25861380.20992849X-RAY DIFFRACTION92
2.0182-2.04370.26151630.19422809X-RAY DIFFRACTION93
2.0437-2.07060.25761290.19062861X-RAY DIFFRACTION93
2.0706-2.0990.24071440.18732876X-RAY DIFFRACTION94
2.099-2.1290.24141610.18942859X-RAY DIFFRACTION94
2.129-2.16070.25711570.18112958X-RAY DIFFRACTION95
2.1607-2.19450.26351440.18382943X-RAY DIFFRACTION96
2.1945-2.23050.26191650.182922X-RAY DIFFRACTION97
2.2305-2.26890.23921680.17032973X-RAY DIFFRACTION97
2.2689-2.31010.23111780.16873033X-RAY DIFFRACTION98
2.3101-2.35460.24081440.17372935X-RAY DIFFRACTION97
2.3546-2.40260.23611620.1722981X-RAY DIFFRACTION98
2.4026-2.45480.22781510.16752995X-RAY DIFFRACTION98
2.4548-2.51190.24751620.16443038X-RAY DIFFRACTION98
2.5119-2.57470.23261610.16522941X-RAY DIFFRACTION98
2.5747-2.64430.20331730.17292996X-RAY DIFFRACTION98
2.6443-2.72210.21841650.16363018X-RAY DIFFRACTION98
2.7221-2.80990.24421600.17163000X-RAY DIFFRACTION98
2.8099-2.91020.24961710.17382972X-RAY DIFFRACTION98
2.9102-3.02670.23241540.17583004X-RAY DIFFRACTION98
3.0267-3.16430.22361490.16163030X-RAY DIFFRACTION98
3.1643-3.33090.21591730.15212959X-RAY DIFFRACTION98
3.3309-3.53940.18191450.13773052X-RAY DIFFRACTION98
3.5394-3.81220.15911450.12483002X-RAY DIFFRACTION98
3.8122-4.19510.13951750.11193007X-RAY DIFFRACTION99
4.1951-4.80030.13261660.10312988X-RAY DIFFRACTION98
4.8003-6.04090.15641570.12073030X-RAY DIFFRACTION99
6.0409-31.5490.1691650.13682980X-RAY DIFFRACTION97
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)
11.2730.0664-0.09940.9359-0.23781.21610.0232-0.11820.10410.12640.0530.2064-0.0446-0.0926-0.06520.1470.02710.04480.1680.02130.2067-15.05786.9719.7734
21.16790.3632-0.0120.4561-0.0480.5477-0.0093-0.0871-0.25590.01230.0253-0.00490.0897-0.0274-0.01950.15720.01960.00880.14320.02270.1881.0885-11.403717.3466
31.14550.4568-0.14931.4810.06241.22120.1-0.4536-0.16280.1919-0.0788-0.1129-0.07270.2424-0.00720.2417-0.0035-0.03510.39920.04260.192619.824-2.197534.0614
41.053-0.0754-0.02760.82030.15371.1623-0.03730.2505-0.088-0.05980.0736-0.08430.04510.1016-0.02520.1913-0.0237-0.01830.2716-0.04050.18316.2033-5.5001-19.4327
50.49290.093-0.09030.6023-0.04550.4353-0.04110.27450.0547-0.15020.06480.18660.0274-0.1497-0.0280.2264-0.0473-0.05580.38790.06730.2231-13.45765.696-26.1146
60.77970.162-0.0760.9176-0.32370.9048-0.06180.2291-0.0892-0.10110.0690.03550.1372-0.0493-0.01170.2443-0.0628-0.05560.3291-0.02850.1786-13.218-11.1661-20.7362
71.0121-0.0660.05121.05730.07360.6218-0.04880.4205-0.0575-0.22970.1182-0.04630.20040.0281-0.02310.2837-0.0432-0.03240.366-0.06160.1815-2.6457-9.0427-30.2063
80.80240.0360.07770.4746-0.01330.9788-0.03050.15160.1038-0.02070.04120.0614-0.0768-0.0188-0.01940.1828-0.0146-0.00810.19570.04420.18162.535316.2871-10.614
91.16810.17040.28250.351-0.20061.0025-0.01010.26040.2673-0.12970.00340.0435-0.37690.03350.01320.3217-0.034-0.02060.30460.12580.29444.843831.1437-23.3687
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 139 )
2X-RAY DIFFRACTION2chain 'A' and (resid 140 through 608 )
3X-RAY DIFFRACTION3chain 'A' and (resid 609 through 663 )
4X-RAY DIFFRACTION4chain 'B' and (resid -1 through 139 )
5X-RAY DIFFRACTION5chain 'B' and (resid 140 through 282 )
6X-RAY DIFFRACTION6chain 'B' and (resid 283 through 349 )
7X-RAY DIFFRACTION7chain 'B' and (resid 350 through 393 )
8X-RAY DIFFRACTION8chain 'B' and (resid 394 through 608 )
9X-RAY DIFFRACTION9chain 'B' and (resid 609 through 663 )

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