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- PDB-5i23: Crystal Structure of Agd31B, alpha-transglucosylase in Glycoside ... -

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Basic information

Entry
Database: PDB / ID: 5i23
TitleCrystal Structure of Agd31B, alpha-transglucosylase in Glycoside Hydrolase Family 31, in complex with Cyclophellitol Aziridine probe CF022
ComponentsOligosaccharide 4-alpha-D-glucosyltransferase
KeywordsTRANSFERASE / 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-66V / Oligosaccharide 4-alpha-D-glucosyltransferase
Similarity search - Component
Biological speciesCellvibrio japonicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)95,83511
Polymers94,5931
Non-polymers1,24210
Water11,367631
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-54 kcal/mol
Surface area28550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)198.000, 198.000, 103.000
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)
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 , 5 types, 641 molecules

#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-66V / 1-(8-{[(1S,2R,3S,4S,5R,6R)-2,3,4,5-tetrahydroxy-6-(hydroxymethyl)cyclohexyl]amino}octyl)triaza-1,2-dien-2-ium


Mass: 347.430 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H31N4O5
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 631 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.3 Å3/Da / Density % sol: 62.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 1.8 M AMMONIUM SULFATE, 0.1 M HEPES (PH 7.0), 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: Feb 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.95→171.47 Å / Num. obs: 86417 / % possible obs: 100 % / Redundancy: 20 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 19.6
Reflection shellResolution: 1.95→1.99 Å / Redundancy: 20.1 % / Rmerge(I) obs: 1.64 / Mean I/σ(I) obs: 0.801 / % 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: 1.95→171.47 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 6.014 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.108 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18711 4304 5 %RANDOM
Rwork0.16254 ---
obs0.16375 82110 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 35.753 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å2-0.12 Å2-0 Å2
2---0.24 Å20 Å2
3---0.78 Å2
Refinement stepCycle: LAST / Resolution: 1.95→171.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6229 0 74 631 6934
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196530
X-RAY DIFFRACTIONr_bond_other_d0.0020.026054
X-RAY DIFFRACTIONr_angle_refined_deg1.5731.9568855
X-RAY DIFFRACTIONr_angle_other_deg0.967313940
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7145791
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.83223.805318
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.34151065
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.711542
X-RAY DIFFRACTIONr_chiral_restr0.0950.2929
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217433
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021584
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_it0.9251.9753149
X-RAY DIFFRACTIONr_mcbond_other0.921.9743148
X-RAY DIFFRACTIONr_mcangle_it1.4582.9543945
X-RAY DIFFRACTIONr_mcangle_other1.4582.9553946
X-RAY DIFFRACTIONr_scbond_it1.5272.223381
X-RAY DIFFRACTIONr_scbond_other1.5272.223381
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5063.244911
X-RAY DIFFRACTIONr_long_range_B_refined6.16117.0677740
X-RAY DIFFRACTIONr_long_range_B_other6.1617.0687741
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 329 -
Rwork0.247 5976 -
obs--99.92 %
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)
11.05-0.73580.41121.9036-0.64733.12430.12910.14950.1039-0.4368-0.1576-0.2508-0.11180.18630.02840.16330.07950.13050.16950.19460.252231.0597153.657699.6719
20.0262-0.06850.02810.24980.01240.42920.02330.02430.0097-0.0263-0.079-0.0478-0.0353-0.00070.05570.0702-0.0117-0.07390.10120.15320.291820.9643152.0496130.6988
30.4254-0.13510.53091.4854-0.42952.01420.0176-0.0068-0.0255-0.0531-0.0286-0.0408-0.20560.03740.0110.1224-0.0462-0.09320.09230.16770.310124.7507167.6222134.2221
40.1004-0.18340.01470.42390.07240.13410.0340.0371-0.0149-0.0502-0.08920.0279-0.0177-0.00350.05510.057-0.014-0.08170.09580.13570.293621.9972136.8472133.458
50.9080.49680.01041.81270.04250.2599-0.03760.0820.076-0.0068-0.0234-0.01190.03680.05670.06110.02890.0071-0.02170.07440.11330.229539.0898114.3791136.8838
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A35 - 143
2X-RAY DIFFRACTION2A144 - 359
3X-RAY DIFFRACTION3A360 - 422
4X-RAY DIFFRACTION4A423 - 717
5X-RAY DIFFRACTION5A718 - 817

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