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- PDB-3weo: Sugar beet alpha-glucosidase with acarviosyl-maltohexaose -

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Basic information

Entry
Database: PDB / ID: 3weo
TitleSugar beet alpha-glucosidase with acarviosyl-maltohexaose
ComponentsAlpha-glucosidase
KeywordsHYDROLASE / alpha-glucosidase / glycoside hydrolase family 31 / (beta/alpha)8-barrel / acarbose derivative
Function / homology
Function and homology information


alpha-glucosidase / maltose alpha-glucosidase activity / carbohydrate binding
Similarity search - Function
: / Glycosyl hydrolases family 31, conserved site / Glycosyl hydrolases family 31 signature 2. / glycosyl hydrolase (family 31) / 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 ...: / Glycosyl hydrolases family 31, conserved site / Glycosyl hydrolases family 31 signature 2. / glycosyl hydrolase (family 31) / 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 / 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
Biological speciesBeta vulgaris (beet)
MethodX-RAY DIFFRACTION / SYNCHROTRON / rigid body refinement / Resolution: 1.45 Å
AuthorsTagami, T. / Yamashita, K. / Okuyama, M. / Mori, H. / Yao, M. / Kimura, A.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structural advantage of sugar beet alpha-glucosidase to stabilize the Michaelis complex with long-chain substrate
Authors: Tagami, T. / Yamashita, K. / Okuyama, M. / Mori, H. / Yao, M. / Kimura, A.
History
DepositionJul 9, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Other
Revision 1.2Dec 31, 2014Group: Database references
Revision 1.3Feb 4, 2015Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / 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_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,2117
Polymers102,5121
Non-polymers2,6986
Water18,5011027
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.166, 99.154, 107.354
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Alpha-glucosidase /


Mass: 102512.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: seeds / Source: (natural) Beta vulgaris (beet) / Strain: cv. Abend / References: UniProt: L0N7E5, alpha-glucosidase

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Sugars , 4 types, 4 molecules

#2: Polysaccharide alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[DGlcpNAcb1-4]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-1/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Polysaccharide 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D- ...4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1294.169 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,7,6/[a2122h-1a_1-5][a2122m-1a_1-5_4*NC^SC^SC^SC^RCCO/7=^ZC$3/6O/5O/4O]/1-1-1-1-1-1-2/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-6-deoxy-Glcp4N]{[(4+1)][<C7O4>]{}}}}}}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 1029 molecules

#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1027 / 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: 2.24 Å3/Da / Density % sol: 45.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 50mM ammonium sulfate, 50mM sodium acetate buffer, 18% PEG monomethylether 2000, 4.44mM acarviosyl-maltohexaose, pH 4.5, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: May 26, 2012
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→42.972 Å / Num. obs: 162274 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 3.66 % / Biso Wilson estimate: 12.83 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.02
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.45-1.540.4982.46199.3
1.54-1.640.3293.64199.9
1.64-1.770.2235.17199.9
1.77-1.940.1467.41199.8
1.94-2.170.10910199.8
2.17-2.510.09212.2199.7
2.51-3.070.08214.01199.5
3.07-4.330.07615.76199.1
4.330.07415.89195.8

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
BSSdata collection
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: rigid body refinement
Starting model: PDB ENTRY 3W37

3w37


Resolution: 1.45→42.972 Å / Occupancy max: 1 / Occupancy min: 0.12 / FOM work R set: 0.9353 / SU ML: 0.11 / σ(F): 1.34 / Phase error: 12.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1499 3358 2.07 %
Rwork0.1234 --
obs0.1239 162108 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.05 Å2 / Biso mean: 19.2045 Å2 / Biso min: 6.43 Å2
Refinement stepCycle: LAST / Resolution: 1.45→42.972 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6587 0 179 1027 7793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087238
X-RAY DIFFRACTIONf_angle_d1.3089912
X-RAY DIFFRACTIONf_dihedral_angle_d15.9952685
X-RAY DIFFRACTIONf_chiral_restr0.1561096
X-RAY DIFFRACTIONf_plane_restr0.0071271
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.45-1.47070.20531350.181565406675100
1.4707-1.49270.19471320.168665976729100
1.4927-1.5160.2051540.152265476701100
1.516-1.54090.16591440.140565786722100
1.5409-1.56740.16411600.130865616721100
1.5674-1.59590.16681420.125965626704100
1.5959-1.62660.1651430.118965936736100
1.6266-1.65980.1581320.116866046736100
1.6598-1.69590.15151310.112665416672100
1.6959-1.73540.14931430.105965976740100
1.7354-1.77880.13971360.100465906726100
1.7788-1.82690.13231350.096266196754100
1.8269-1.88060.12221350.094766166751100
1.8806-1.94130.1471440.099665836727100
1.9413-2.01070.13151380.101166066744100
2.0107-2.09120.13671310.104166416772100
2.0912-2.18640.12591420.102266296771100
2.1864-2.30170.14921400.105766126752100
2.3017-2.44580.13221350.109766346769100
2.4458-2.63470.13931430.11486645678899
2.6347-2.89980.1421440.124466666810100
2.8998-3.31920.15091350.132967276862100
3.3192-4.18130.15641420.13236702684499
4.1813-42.99070.16211420.15736760690296

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