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- PDB-3wen: Sugar beet alpha-glucosidase with acarviosyl-maltopentaose -

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Basic information

Entry
Database: PDB / ID: 3wen
TitleSugar beet alpha-glucosidase with acarviosyl-maltopentaose
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 / MOLECULAR REPLACEMENT / Resolution: 2.59 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: 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

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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)104,7536
Polymers102,5121
Non-polymers2,2415
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.352, 138.872, 148.976
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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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 , 3 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 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


Type: oligosaccharide / Mass: 1132.028 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,6,5/[a2122h-1a_1-5][a2122m-1a_1-5_4*NC^SC^SC^SC^RCCO/7=^ZC$3/6O/5O/4O]/1-1-1-1-1-2/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 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-6-deoxy-Glcp4N]{[(4+1)][<C7O4>]{}}}}}}}LINUCSPDB-CARE
#4: 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.: 2
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 , 2 types, 176 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.46 Å3/Da / Density % sol: 49.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 50mM ammonium sulfate, 50mM sodium acetate buffer, 17% PEG monomethylether 2000, 7.79mM acarviosyl-maltopentaose, 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: Jan 30, 2012
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.59→44.206 Å / Num. obs: 31018 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 5.61 % / Biso Wilson estimate: 47.701 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 15.04
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
2.59-2.750.6810.6393.2226738509348620.7195.5
2.75-2.930.4390.4434.7226949474946920.4998.8
2.93-3.170.2610.2637.5225306446244040.29198.7
3.17-3.470.1460.15311.8723044410540400.16998.4
3.47-3.880.0740.09118.4420734373636590.197.9
3.88-4.470.0480.06225.1217914330532290.06897.7
4.47-5.460.0340.04930.4615079281627390.05397.3
5.46-7.660.0320.04730.5811771223921580.05296.4
7.660.0180.03240.156477134012350.03692.2

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
BSSdata collection
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3W37

3w37


Resolution: 2.59→44.206 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8315 / SU ML: 0.3 / σ(F): 1.34 / Phase error: 23.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2451 1576 5.08 %random
Rwork0.1993 ---
obs0.2016 31018 97.44 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.23 Å2 / Biso mean: 37.4489 Å2 / Biso min: 7.88 Å2
Refinement stepCycle: LAST / Resolution: 2.59→44.206 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6606 0 148 175 6929
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036960
X-RAY DIFFRACTIONf_angle_d0.7999505
X-RAY DIFFRACTIONf_chiral_restr0.0551060
X-RAY DIFFRACTIONf_plane_restr0.0041208
X-RAY DIFFRACTIONf_dihedral_angle_d14.7472544
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 (%)
2.5892-2.67270.29941370.24882527266493
2.6727-2.76820.31181410.24672677281899
2.7682-2.87910.31521430.25282691283499
2.8791-3.01010.28651390.23272668280799
3.0101-3.16870.26981680.22382669283799
3.1687-3.36720.26711380.20742687282599
3.3672-3.62710.24631500.19592697284798
3.6271-3.99180.25571170.18282685280298
3.9918-4.5690.21581490.16972694284398
4.569-5.75440.20321400.17412709284997
5.7544-44.21220.21921540.2022738289295
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)
10.004-0.00410.00420.0065-0.00430.00440.02130.0237-0.01190.0459-0.0134-0.00830.02820.01890.00090.27470.0860.00060.12140.06230.231724.494-2.107258.991
20.16140.04380.09540.03560.01150.12020.08130.34460.1477-0.0233-0.02230.02930.00690.09960.16920.18410.04340.09240.23030.36190.167721.956226.192641.2571
30.0114-0.00830.01060.0076-0.0050.01280.0250.03370.0067-0.02480.01230.04570.00930.01830.02550.25310.0629-0.04050.36840.17860.2255-0.670118.612120.7643
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 40:192 )A40 - 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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