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

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Basic information

Entry
Database: PDB / ID: 5npb
TitleCrystal Structure of cjAgd31B (alpha-transglucosylase from Glycoside Hydrolase Family 31) in complex with alpha Cyclophellitol Cyclosulfate probe ME647
ComponentsOligosaccharide 4-alpha-D-glucosyltransferase
KeywordsHYDROLASE
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-93Z / OXALATE ION / Oligosaccharide 4-alpha-D-glucosyltransferase
Similarity search - Component
Biological speciesCellvibrio japonicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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: 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 / Refinement description / Category: citation / citation_author / software
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 / _software.classification
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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)95,6309
Polymers94,5931
Non-polymers1,0378
Water9,044502
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, 1 peak containing protein
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-46 kcal/mol
Surface area28650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)197.380, 197.380, 102.909
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 (bacteria) / Gene: agd31B, CJA_3248 / Production host: Escherichia coli (E. coli)
References: UniProt: B3PEE6, oligosaccharide 4-alpha-D-glucosyltransferase

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Non-polymers , 5 types, 510 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#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-93Z / [(1~{S},2~{R},3~{R},4~{S},5~{R})-2-(hydroxymethyl)-3,4,5,6-tetrakis(oxidanyl)cyclohexyl] hydrogen sulfate


Mass: 274.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H14O9S
#5: Chemical ChemComp-OXL / OXALATE ION


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


Mass: 18.015 Da / Num. of mol.: 502 / 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: 3.06 Å3/Da / Density % sol: 59.79 %
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: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→49.85 Å / Num. obs: 92616 / % possible obs: 100 % / Redundancy: 24.1 % / CC1/2: 1 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.016 / Net I/σ(I): 30.2
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 24.1 % / Rmerge(I) obs: 0.755 / Mean I/σ(I) obs: 5.5 / Num. unique obs: 4491 / CC1/2: 0.959 / Rpim(I) all: 0.156 / % 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: 1.9→49.85 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.265 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.123 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22785 4584 4.9 %RANDOM
Rwork0.19609 ---
obs0.19769 88031 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.902 Å2
Baniso -1Baniso -2Baniso -3
1--1.4 Å2-0.7 Å20 Å2
2---1.4 Å20 Å2
3---4.54 Å2
Refinement stepCycle: 1 / Resolution: 1.9→49.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6236 0 60 502 6798
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0196533
X-RAY DIFFRACTIONr_bond_other_d0.0020.025858
X-RAY DIFFRACTIONr_angle_refined_deg1.6731.9568870
X-RAY DIFFRACTIONr_angle_other_deg1.003313615
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8745794
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.23123.805318
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.122151067
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7221542
X-RAY DIFFRACTIONr_chiral_restr0.10.2933
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217314
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021400
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_it2.2673.0253158
X-RAY DIFFRACTIONr_mcbond_other2.2633.0253157
X-RAY DIFFRACTIONr_mcangle_it3.1954.5243958
X-RAY DIFFRACTIONr_mcangle_other3.1954.5243959
X-RAY DIFFRACTIONr_scbond_it2.8963.3473375
X-RAY DIFFRACTIONr_scbond_other2.8933.3453368
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5264.8844907
X-RAY DIFFRACTIONr_long_range_B_refined6.2134.8347292
X-RAY DIFFRACTIONr_long_range_B_other6.20934.8287292
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 307 -
Rwork0.317 6425 -
obs--99.85 %

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