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- PDB-5i24: Crystal Structure of Agd31B, alpha-transglucosylase in Glycoside ... -

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Basic information

Entry
Database: PDB / ID: 5i24
TitleCrystal Structure of Agd31B, alpha-transglucosylase in Glycoside Hydrolase Family 31, in complex with Cyclophellitol Aziridine probe CF021
ComponentsOligosaccharide 4-alpha-D-glucosyltransferase
KeywordsHYDROLASE / Alpha glycosidase / Cyclophellitol Aziridine / Inhibitor / Probe
Function / homology
Function and homology information


oligosaccharide 4-alpha-D-glucosyltransferase / oligosaccharide 4-alpha-D-glucosyltransferase activity / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
: / Domain of unknown function DUF5110 / Domain of unknown function (DUF5110) / glycosyl hydrolase (family 31) / 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 ...: / Domain of unknown function DUF5110 / Domain of unknown function (DUF5110) / glycosyl hydrolase (family 31) / 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
Chem-66U / Oligosaccharide 4-alpha-D-glucosyltransferase
Similarity search - Component
Biological speciesCellvibrio japonicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsWu, L. / Davies, G.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Research CouncilERC-2012-AdG-322942 United Kingdom
CitationJournal: Acs Cent.Sci. / Year: 2016
Title: Detection of Active Mammalian GH31 alpha-Glucosidases in Health and Disease Using In-Class, Broad-Spectrum Activity-Based Probes.
Authors: Jiang, J. / Kuo, C.L. / Wu, L. / Franke, C. / Kallemeijn, W.W. / Florea, B.I. / van Meel, E. / van der Marel, G.A. / Codee, J.D. / Boot, R.G. / Davies, G.J. / Overkleeft, H.S. / Aerts, J.M.
History
DepositionFeb 8, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.3Jan 10, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Oligosaccharide 4-alpha-D-glucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,76912
Polymers94,5931
Non-polymers1,17611
Water11,440635
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-42 kcal/mol
Surface area28750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)197.300, 197.300, 102.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Oligosaccharide 4-alpha-D-glucosyltransferase / / Alpha-glucosidase 31B / CJAgd31B


Mass: 94592.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cellvibrio japonicus (strain Ueda107) (bacteria)
Strain: Ueda107 / Gene: agd31B, CJA_3248 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B3PEE6, oligosaccharide 4-alpha-D-glucosyltransferase

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Non-polymers , 6 types, 646 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-66U / (1R,2S,3S,4R,5S,6R)-5-amino-6-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol


Mass: 193.198 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15NO5
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 635 / 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: 3.06 Å3/Da / Density % sol: 59.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 1.8 M AMMONIUM SULFATE, 0.1 M HEPES (PH7.0), 2% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.85→170.87 Å / Num. obs: 100134 / % possible obs: 100 % / Redundancy: 24.5 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 26.8
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 25 % / Rmerge(I) obs: 1.21 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4B9Y

4b9y


Resolution: 1.85→170.87 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.964 / SU B: 5.753 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.096 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18813 4899 4.9 %RANDOM
Rwork0.16905 ---
obs0.17002 95234 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 34.16 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å2-0.23 Å2-0 Å2
2---0.45 Å20 Å2
3---1.47 Å2
Refinement stepCycle: 1 / Resolution: 1.85→170.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6229 0 70 635 6934
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0196498
X-RAY DIFFRACTIONr_bond_other_d0.0020.026035
X-RAY DIFFRACTIONr_angle_refined_deg1.5831.9568808
X-RAY DIFFRACTIONr_angle_other_deg0.976313887
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5975785
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.37423.766316
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.101151060
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9441542
X-RAY DIFFRACTIONr_chiral_restr0.0950.2926
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217375
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021573
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_it0.7541.5613135
X-RAY DIFFRACTIONr_mcbond_other0.7471.563133
X-RAY DIFFRACTIONr_mcangle_it1.2012.3343921
X-RAY DIFFRACTIONr_mcangle_other1.2012.3343922
X-RAY DIFFRACTIONr_scbond_it1.2291.7613363
X-RAY DIFFRACTIONr_scbond_other1.2251.7613363
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0132.5724888
X-RAY DIFFRACTIONr_long_range_B_refined6.20413.8587699
X-RAY DIFFRACTIONr_long_range_B_other6.19713.8487697
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 357 -
Rwork0.269 6964 -
obs--99.97 %
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)
11.6047-0.47760.62272.0163-0.0443.24890.08920.23220.1727-0.3866-0.1574-0.3707-0.20830.31020.06810.19420.05320.1050.16650.21910.362531.2255153.701399.6395
20.0922-0.10280.03810.2993-0.01030.6340.01190.0209-0.018-0.0405-0.1074-0.1029-0.08920.00790.09550.0931-0.0258-0.10720.09530.16380.351421.2178152.7637130.7009
35.1434-0.03681.11353.0957-0.32623.3390.06520.03210.0838-0.2141-0.2079-0.069-0.5726-0.02180.14270.2713-0.0302-0.14780.07660.12690.2622.3956172.973131.2053
40.1257-0.24810.03580.58380.04450.32220.01430.0299-0.0205-0.0417-0.1065-0.0174-0.04380.02630.09220.0595-0.0312-0.10180.09080.1560.342622.6113139.644133.7504
51.57460.7299-0.09112.58960.06850.7354-0.09480.13530.0968-0.0274-0.0323-0.00430.06490.10560.12710.02920.004-0.0190.10080.14860.283739.3635114.6469136.7388
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A35 - 143
2X-RAY DIFFRACTION2A144 - 363
3X-RAY DIFFRACTION3A364 - 392
4X-RAY DIFFRACTION4A393 - 717
5X-RAY DIFFRACTION5A718 - 817

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