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- PDB-3wel: Sugar beet alpha-glucosidase with acarviosyl-maltotriose -

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Basic information

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


: / alpha-glucosidase / 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: 1.84 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 8, 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: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / 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 / 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 / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list
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
Revision 2.2Oct 30, 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: Alpha-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,7417
Polymers102,5121
Non-polymers2,2296
Water10,881604
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.705, 97.886, 106.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 , 2 types, 3 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.: 2
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 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


Type: oligosaccharide / Mass: 807.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,4,3/[a2122h-1a_1-5][a2122m-1a_1-5_4*NC^SC^SC^SC^RCCO/7=^ZC$3/6O/5O/4O]/1-1-1-2/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][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

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Non-polymers , 3 types, 607 molecules

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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 604 / 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: 2.16 Å3/Da / Density % sol: 43.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 50mM ammonium sulfate, 50mM sodium acetate buffer, 17% PEG monomethylether 2000, 33.3mM acarviosyl-maltotriose, 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: 1.84→38.87 Å / Num. obs: 77140 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.55 % / Biso Wilson estimate: 29.077 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 9.16
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.84-1.950.8780.6692.014229612456119290.78895.8
1.95-2.080.5290.4213.274257011770117300.49499.7
2.08-2.250.3530.294.873938210930108580.3499.3
2.25-2.460.240.2066.693623210070100320.24199.6
2.46-2.750.1650.1449.2532909920391570.16999.5
2.75-3.180.1010.09312.8728563812980720.10999.3
3.18-3.880.0550.05618.9123641691768560.06699.1
3.88-5.480.0350.0424.2118307543753760.04898.9
5.480.0320.03624.3110277318131300.04398.4

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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: 1.84→38.87 Å / Occupancy max: 1 / Occupancy min: 0.21 / FOM work R set: 0.8737 / SU ML: 0.18 / σ(F): 1.35 / Phase error: 19.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1975 1572 2.04 %random
Rwork0.1724 ---
obs0.1729 77132 98.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.51 Å2 / Biso mean: 25.3559 Å2 / Biso min: 6.67 Å2
Refinement stepCycle: LAST / Resolution: 1.84→38.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6587 0 148 604 7339
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077092
X-RAY DIFFRACTIONf_angle_d1.149693
X-RAY DIFFRACTIONf_chiral_restr0.081069
X-RAY DIFFRACTIONf_plane_restr0.0051241
X-RAY DIFFRACTIONf_dihedral_angle_d15.982613
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8362-1.89550.29751230.24596364648793
1.8955-1.96320.22371470.214768687015100
1.9632-2.04180.22331480.196668446992100
2.0418-2.13480.2061400.18756850699099
2.1348-2.24730.24861420.18246843698599
2.2473-2.38810.22991460.176268787024100
2.3881-2.57240.1781420.17269057047100
2.5724-2.83120.23471430.165169037046100
2.8312-3.24080.19691460.15746943708999
3.2408-4.08230.16451480.14826961710999
4.0823-38.87880.16931470.17477201734899
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0312-0.0117-0.01090.0108-0.01460.00980.0709-0.1138-0.02550.08420.0565-0.2006-0.1450.40850.03070.0546-0.1866-0.02620.5461-0.1330.247140.1761-8.8719-18.2847
20.3170.0528-0.06280.61980.30660.5427-0.0354-0.0036-0.0121-0.02470.02180.051-0.07590.0669-0.01680.0736-0.02620.020.06730.0030.07518.4405-14.4496-25.703
30.10220.03840.04720.08250.06650.0364-0.00720.2487-0.2579-0.12050.1374-0.06260.08950.20550.06530.1587-0.05310.11860.0542-0.08470.022810.6048-37.3287-46.8943
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 38:192 )A38 - 192
2X-RAY DIFFRACTION2chain 'A' and (resseq 193:738 )A193 - 738
3X-RAY DIFFRACTION3chain 'A' and (resseq 739:909 )A739 - 909

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