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- PDB-5npd: Crystal Structure of D412N nucleophile mutant cjAgd31B (alpha-tra... -

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Basic information

Entry
Database: PDB / ID: 5npd
TitleCrystal Structure of D412N nucleophile mutant cjAgd31B (alpha-transglucosylase from Glycoside Hydrolase Family 31) in complex with alpha Cyclophellitol Aziridine probe CF021
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-94B / 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 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)95,96317
Polymers94,4611
Non-polymers1,50216
Water8,863492
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, one symmetrical peak containing protein
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-64 kcal/mol
Surface area29150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)197.312, 197.312, 102.772
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: 94460.523 Da / Num. of mol.: 1 / Mutation: D412N
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 , 6 types, 508 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-94B / (1~{S},2~{S},3~{S},4~{R},5~{R},6~{S})-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


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


Mass: 18.015 Da / Num. of mol.: 492 / 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: 59.76 %
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: Jul 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.95→47.39 Å / Num. obs: 85623 / % possible obs: 100 % / Redundancy: 20.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.023 / Net I/σ(I): 21.7
Reflection shellResolution: 1.95→1.99 Å / Redundancy: 20.3 % / Rmerge(I) obs: 1.408 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 4474 / CC1/2: 0.899 / Rpim(I) all: 0.32 / % 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→47.39 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.958 / SU B: 4.356 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.121 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20994 4331 5.1 %RANDOM
Rwork0.17095 ---
obs0.17291 81290 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.926 Å2
Baniso -1Baniso -2Baniso -3
1--1.78 Å2-0.89 Å2-0 Å2
2---1.78 Å2-0 Å2
3---5.76 Å2
Refinement stepCycle: 1 / Resolution: 1.95→47.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6236 0 90 492 6818
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0196525
X-RAY DIFFRACTIONr_bond_other_d0.0020.025870
X-RAY DIFFRACTIONr_angle_refined_deg1.6041.9598843
X-RAY DIFFRACTIONr_angle_other_deg0.991313634
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7575790
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.76323.778315
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.792151062
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5791542
X-RAY DIFFRACTIONr_chiral_restr0.0980.2931
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217265
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021393
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_it2.3473.4883145
X-RAY DIFFRACTIONr_mcbond_other2.3463.4873144
X-RAY DIFFRACTIONr_mcangle_it3.2735.2183937
X-RAY DIFFRACTIONr_mcangle_other3.2735.2183938
X-RAY DIFFRACTIONr_scbond_it3.3183.8883379
X-RAY DIFFRACTIONr_scbond_other3.3183.8863375
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1735.6644897
X-RAY DIFFRACTIONr_long_range_B_refined6.5940.0287235
X-RAY DIFFRACTIONr_long_range_B_other6.58940.037236
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
Rfree0.339 296 -
Rwork0.298 5930 -
obs--99.9 %

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