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- PDB-5dkz: Crystal structure of glucosidase II alpha subunit (alpha3-Glc2-bo... -

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Basic information

Entry
Database: PDB / ID: 5dkz
TitleCrystal structure of glucosidase II alpha subunit (alpha3-Glc2-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 / endoplasmic reticulum
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
alpha-nigerose / alpha-glucosidase
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 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: chem_comp / diffrn_source / pdbx_struct_oper_list
Item: _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_mod_residue / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.type_symbol / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_mod_residue.auth_asym_id / _pdbx_struct_mod_residue.auth_seq_id / _pdbx_struct_mod_residue.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha glucosidase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,7992
Polymers108,4571
Non-polymers3421
Water5,314295
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint7 kcal/mol
Surface area32850 Å2
Unit cell
Length a, b, c (Å)189.947, 189.947, 158.642
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Alpha glucosidase-like protein


Mass: 108457.148 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 31-977 / Mutation: D556A
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) / References: UniProt: G0SG42
#2: Polysaccharide alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose / alpha-nigerose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-nigerose
DescriptorTypeProgram
DGlcpa1-3DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a3-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(3+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.54 Å3/Da / Density % sol: 51.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.2 M sodium citrate tribasic, 0.1 M Tris-HCl (pH 8.0), 5 mM alpha3-Glc2 soaking

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 43022 / Num. obs: 43005 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 33.5
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 6.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.943 / SU B: 6.366 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R: 0.321 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.199 2038 4.8 %RANDOM
Rwork0.148 ---
obs0.15 40816 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.844 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å2-0.19 Å20 Å2
2---0.39 Å20 Å2
3---1.26 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7427 0 23 295 7745
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0197671
X-RAY DIFFRACTIONr_bond_other_d0.0010.027067
X-RAY DIFFRACTIONr_angle_refined_deg1.3391.93810398
X-RAY DIFFRACTIONr_angle_other_deg0.756316296
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_restr0.0740.21075
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218640
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021847
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_it1.9413.2143681
X-RAY DIFFRACTIONr_mcbond_other1.9373.2133680
X-RAY DIFFRACTIONr_mcangle_it3.0254.8114596
X-RAY DIFFRACTIONr_mcangle_other3.0264.8114597
X-RAY DIFFRACTIONr_scbond_it2.4633.4953990
X-RAY DIFFRACTIONr_scbond_other2.4633.4953990
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1155.1045803
X-RAY DIFFRACTIONr_long_range_B_refined4.80931.9086753
X-RAY DIFFRACTIONr_long_range_B_other4.80831.9776666
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 132 -
Rwork0.192 2971 -
obs--100 %

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