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- PDB-7p4d: Crystal Structure of Agd31B, alpha-transglucosylase in Glycoside ... -

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Basic information

Entry
Database: PDB / ID: 7p4d
TitleCrystal Structure of Agd31B, alpha-transglucosylase in Glycoside Hydrolase Family 31, in complex with covalent Cyclophellitol Sulfamidate probe KK130
ComponentsOligosaccharide 4-alpha-D-glucosyltransferase
KeywordsHYDROLASE / glycoside hydrolase / GH31 / inhibitor / carbohydrate
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) / 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 / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Chem-56I / OXALATE ION / Oligosaccharide 4-alpha-D-glucosyltransferase
Similarity search - Component
Biological speciesCellvibrio japonicus Ueda107 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsWu, L. / Davies, G.J.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)AdG-322942European Union
CitationJournal: J.Am.Chem.Soc. / Year: 2022
Title: 1,6- epi-Cyclophellitol Cyclosulfamidate Is a Bona Fide Lysosomal alpha-Glucosidase Stabilizer for the Treatment of Pompe Disease.
Authors: Kok, K. / Kuo, C.L. / Katzy, R.E. / Lelieveld, L.T. / Wu, L. / Roig-Zamboni, V. / van der Marel, G.A. / Codee, J.D.C. / Sulzenbacher, G. / Davies, G.J. / Overkleeft, H.S. / Aerts, J.M.F.G. / Artola, M.
History
DepositionJul 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2022Group: Database references / Category: citation / citation_author
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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Jul 31, 2024Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Source and taxonomy
Category: atom_site / chem_comp ...atom_site / chem_comp / entity_src_gen / pdbx_audit_support
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.type / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_audit_support.country
Revision 2.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)96,02514
Polymers94,5931
Non-polymers1,43213
Water8,737485
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, protein monomer elutes as a single peak from SEC
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-62 kcal/mol
Surface area28780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)197.076, 197.076, 102.149
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number177
Space group name H-MP622
Components on special symmetry positions
IDModelComponents
11AAA-1483-

HOH

21AAA-1484-

HOH

31AAA-1485-

HOH

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Components

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Protein , 1 types, 1 molecules AAA

#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 Ueda107 (bacteria)
Strain: Ueda107 / Gene: agd31B, CJA_3248 / Production host: Escherichia coli (E. coli)
References: UniProt: B3PEE6, oligosaccharide 4-alpha-D-glucosyltransferase

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Non-polymers , 6 types, 498 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


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


Mass: 88.019 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2O4
#5: Chemical ChemComp-56I / [(1R,2R,3R,4R,5S)-2-(hydroxymethyl)-3,4,5-tris(oxidanyl)cyclohexyl]sulfamic acid


Mass: 257.261 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15NO7S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 485 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.24 Å3/Da / Density % sol: 62.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / 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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.85→98.54 Å / Num. obs: 99190 / % possible obs: 100 % / Redundancy: 24.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.027 / Rrim(I) all: 0.136 / Net I/σ(I): 14.2
Reflection shellResolution: 1.85→1.88 Å / Rmerge(I) obs: 2.685 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4849 / CC1/2: 0.696 / Rpim(I) all: 0.545 / Rrim(I) all: 2.741

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
xia2data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4b9y

4b9y


Resolution: 1.85→98.538 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / Cross valid method: FREE R-VALUE / ESU R: 0.113 / ESU R Free: 0.112
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2216 4583 4.621 %
Rwork0.1884 94592 -
all0.19 --
obs-99175 99.947 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 39.213 Å2
Baniso -1Baniso -2Baniso -3
1--1.224 Å2-0.612 Å2-0 Å2
2---1.224 Å20 Å2
3---3.972 Å2
Refinement stepCycle: LAST / Resolution: 1.85→98.538 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6237 0 83 485 6805
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0136518
X-RAY DIFFRACTIONr_bond_other_d0.0350.0175987
X-RAY DIFFRACTIONr_angle_refined_deg1.621.6468842
X-RAY DIFFRACTIONr_angle_other_deg2.3261.57913795
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6875788
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.5122.173359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.676151062
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1691542
X-RAY DIFFRACTIONr_chiral_restr0.080.2814
X-RAY DIFFRACTIONr_chiral_restr_other0.9630.21
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027416
X-RAY DIFFRACTIONr_gen_planes_other0.0140.021572
X-RAY DIFFRACTIONr_nbd_refined0.1990.21196
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2170.25547
X-RAY DIFFRACTIONr_nbtor_refined0.1720.23037
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.22928
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2450
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0320.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1460.213
X-RAY DIFFRACTIONr_nbd_other0.2110.263
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1950.216
X-RAY DIFFRACTIONr_mcbond_it3.4383.8743143
X-RAY DIFFRACTIONr_mcbond_other3.4373.8743142
X-RAY DIFFRACTIONr_mcangle_it4.5445.7923934
X-RAY DIFFRACTIONr_mcangle_other4.5445.7933935
X-RAY DIFFRACTIONr_scbond_it4.2444.3053375
X-RAY DIFFRACTIONr_scbond_other4.1584.2693344
X-RAY DIFFRACTIONr_scangle_it6.3776.284908
X-RAY DIFFRACTIONr_scangle_other6.2636.2254861
X-RAY DIFFRACTIONr_lrange_it7.94243.9397243
X-RAY DIFFRACTIONr_lrange_other7.91443.6857145
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.85-1.8980.354250.34971790.34972420.5310.45999.47530.349
1.898-1.950.2953270.30867080.30770350.7520.7481000.304
1.95-2.0060.2953700.28464960.28568670.7970.80699.98540.275
2.006-2.0680.283500.25463190.25566700.8380.85999.9850.241
2.068-2.1360.2783380.24561540.24764930.8680.87899.98460.229
2.136-2.2110.2832900.23959500.24162410.8610.88899.9840.222
2.211-2.2940.2672910.22257780.22460700.8810.90699.98350.204
2.294-2.3880.2853080.21755450.22158540.8870.91199.98290.199
2.388-2.4940.2582610.21153680.21356320.9130.9299.94670.192
2.494-2.6160.2492520.20450920.20753450.910.92699.98130.186
2.616-2.7570.2462610.20748560.20951190.9240.92999.96090.191
2.757-2.9240.2632340.20546400.20748740.9080.9311000.192
2.924-3.1260.252330.20743370.2145700.9210.9351000.195
3.126-3.3760.2072080.18640540.18742620.9540.9521000.177
3.376-3.6980.192090.16737450.16839540.9560.9631000.161
3.698-4.1330.1781890.14433990.14635880.9620.971000.14
4.133-4.7710.1551440.13230470.13331910.9730.9761000.128
4.771-5.840.1831300.13526190.13827490.9630.9731000.132
5.84-8.2450.223930.16120720.16421650.950.9631000.157
8.245-98.5380.175700.15812330.15913040.9780.97299.92330.168

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