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- PDB-5dky: Crystal structure of glucosidase II alpha subunit (DNJ-bound from) -

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Basic information

Entry
Database: PDB / ID: 5dky
TitleCrystal structure of glucosidase II alpha subunit (DNJ-bound from)
ComponentsAlpha glucosidase-like protein
KeywordsHYDROLASE / ENDOPLASMIC RETICULUM / GLYCOSIDE HYDROLASE / GLYCOSYLATION
Function / homology
Function and homology information


alpha-glucosidase / 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 hydrolases family 31, active site / Glycosyl hydrolases family 31 active site. / 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 hydrolases family 31, active site / Glycosyl hydrolases family 31 active site. / 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
1-DEOXYNOJIRIMYCIN / alpha-glucosidase
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsSatoh, T. / Toshimori, T. / Yan, G. / Yamaguchi, T. / Kato, K.
Funding support Japan, 2items
OrganizationGrant numberCountry
JSPS/MEXT24770102, 25121730 to T.S. and 15H02491, 25102008, 24249002 to K.K. Japan
PRESTO/JST13417569 to T.S. Japan
CitationJournal: Sci Rep / Year: 2016
Title: Structural basis for two-step glucose trimming by glucosidase II involved in ER glycoprotein quality control.
Authors: Satoh, T. / Toshimori, T. / Yan, G. / Yamaguchi, T. / Kato, K.
History
DepositionSep 4, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2016Group: Database references
Revision 1.2Feb 19, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Alpha glucosidase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,6642
Polymers108,5011
Non-polymers1631
Water14,754819
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area370 Å2
ΔGint3 kcal/mol
Surface area32980 Å2
Unit cell
Length a, b, c (Å)189.523, 189.523, 157.784
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-1771-

HOH

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Components

#1: Protein Alpha glucosidase-like protein


Mass: 108501.156 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 31-977
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0064960 / Plasmid: pCold-GST (modified) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: G0SG42
#2: Chemical ChemComp-NOJ / 1-DEOXYNOJIRIMYCIN / MORANOLINE


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: inhibitor*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 819 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.2 M sodium citrate tribasic, 0.1 M Tris-HCl (pH 7.0), 2.5 mM DNJ

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 141836 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 23.6
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 2.8 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.482 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.184 7092 5 %RANDOM
Rwork0.155 ---
obs0.156 133918 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.444 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0.03 Å20 Å2
2---0.05 Å20 Å2
3---0.16 Å2
Refinement stepCycle: 1 / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7485 0 11 819 8315
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0197744
X-RAY DIFFRACTIONr_bond_other_d0.0010.027140
X-RAY DIFFRACTIONr_angle_refined_deg1.4271.93710505
X-RAY DIFFRACTIONr_angle_other_deg0.795316483
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0870.21085
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218757
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021866
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_it1.2551.8513720
X-RAY DIFFRACTIONr_mcbond_other1.2531.8513719
X-RAY DIFFRACTIONr_mcangle_it1.9012.7724649
X-RAY DIFFRACTIONr_mcangle_other1.9012.7734650
X-RAY DIFFRACTIONr_scbond_it1.9342.0584022
X-RAY DIFFRACTIONr_scbond_other1.9342.0584022
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0592.9915850
X-RAY DIFFRACTIONr_long_range_B_refined4.55119.7627357
X-RAY DIFFRACTIONr_long_range_B_other4.23419.336958
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.601→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 516 -
Rwork0.237 9757 -
obs--99.07 %

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