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- PDB-5npe: Crystal Structure of cjAgd31B (alpha-transglucosylase from Glycos... -

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Basic information

Entry
Database: PDB / ID: 5npe
TitleCrystal Structure of cjAgd31B (alpha-transglucosylase from Glycoside Hydrolase Family 31) in complex with beta Cyclophellitol Aziridine probe KY358
ComponentsOligosaccharide 4-alpha-D-glucosyltransferase
KeywordsHYDROLASE
Function / homology
Function and homology information


oligosaccharide 4-alpha-D-glucosyltransferase / oligosaccharide 4-alpha-D-glucosyltransferase activity / alpha-glucosidase activity / N-glycan processing / 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-948 / OXALATE ION / 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.
CitationJournal: ACS Cent Sci / Year: 2017
Title: 1,6-Cyclophellitol Cyclosulfates: A New Class of Irreversible Glycosidase Inhibitor.
Authors: Artola, M. / Wu, L. / Ferraz, M.J. / Kuo, C.L. / Raich, L. / Breen, I.Z. / Offen, W.A. / Codee, J.D.C. / van der Marel, G.A. / Rovira, C. / Aerts, J.M.F.G. / Davies, G.J. / Overkleeft, H.S.
History
DepositionApr 16, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 17, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)95,75112
Polymers94,5931
Non-polymers1,15811
Water10,233568
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, one symmetric peak containing protein
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-70 kcal/mol
Surface area28640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)197.000, 197.000, 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)
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, 579 molecules

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


Mass: 96.063 Da / Num. of mol.: 6 / 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-948 / (1~{R},2~{S},3~{S},4~{R},5~{R},6~{R})-5-(hydroxymethyl)-7-azabicyclo[4.1.0]heptane-2,3,4-triol


Mass: 175.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H13NO4
#6: Chemical ChemComp-OXL / OXALATE ION / Oxalate


Mass: 88.019 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2O4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 568 / 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: 3.05 Å3/Da / Density % sol: 59.67 %
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
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.95→44.43 Å / Num. obs: 85516 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 1 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.022 / Net I/σ(I): 28.8
Reflection shellResolution: 1.95→1.99 Å / Redundancy: 19 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 6.8 / Num. unique obs: 4450 / CC1/2: 0.984 / Rpim(I) all: 0.149 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4b9y

4b9y


Resolution: 1.95→44.43 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.637 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.137 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23656 4293 5 %RANDOM
Rwork0.1912 ---
obs0.19345 81221 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.637 Å2
Baniso -1Baniso -2Baniso -3
1--1.5 Å2-0.75 Å2-0 Å2
2---1.5 Å2-0 Å2
3---4.87 Å2
Refinement stepCycle: 1 / Resolution: 1.95→44.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6236 0 69 568 6873
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0196544
X-RAY DIFFRACTIONr_bond_other_d0.0030.025882
X-RAY DIFFRACTIONr_angle_refined_deg1.7031.9578879
X-RAY DIFFRACTIONr_angle_other_deg1.024313669
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.015796
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.95923.774318
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.009151072
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7061543
X-RAY DIFFRACTIONr_chiral_restr0.1020.2933
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217320
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021403
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_it2.0472.7973160
X-RAY DIFFRACTIONr_mcbond_other2.0432.7973159
X-RAY DIFFRACTIONr_mcangle_it2.9374.1853961
X-RAY DIFFRACTIONr_mcangle_other2.9364.1853962
X-RAY DIFFRACTIONr_scbond_it2.7633.1093384
X-RAY DIFFRACTIONr_scbond_other2.7633.1073380
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3594.5364909
X-RAY DIFFRACTIONr_long_range_B_refined6.06232.3197389
X-RAY DIFFRACTIONr_long_range_B_other6.06232.3157389
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
Rfree0.338 328 -
Rwork0.296 5868 -
obs--99.85 %

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