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- PDB-3w38: Sugar beet alpha-glucosidase -

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Basic information

Entry
Database: PDB / ID: 3w38
TitleSugar beet alpha-glucosidase
ComponentsAlpha-glucosidase
KeywordsHYDROLASE / CARBOHYDRATE / alpha-glucosidase / glycoside hydrolase family 31 / (beta/alpha)8-barrel
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 / molecular replacement / Resolution: 2.79 Å
AuthorsTagami, T. / Yamashita, K. / Okuyama, M. / Mori, H. / Yao, M. / Kimura, A.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Molecular basis for the recognition of long-chain substrates by plant & alpha-glucosidase
Authors: Tagami, T. / Yamashita, K. / Okuyama, M. / Mori, H. / Yao, M. / Kimura, A.
History
DepositionDec 13, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2013Group: Database references
Revision 1.2Jul 17, 2013Group: Database references
Revision 1.3Jul 30, 2014Group: Other
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 / 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.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,4965
Polymers102,5121
Non-polymers9844
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.534, 95.463, 107.651
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

#1: Protein Alpha-glucosidase / / Maltase


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*PLUS, alpha-glucosidase
#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: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / 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
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THE GENEBANK ACCESSION NUMBER IS AB699590 FOR THIS SEQUENCE.

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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: 2.09 Å3/Da / Density % sol: 41.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 100mM ammonium sulfate, 50mM sodium acetate buffer, 18% PEG monomethylether 2000, 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: 2.79→43.67 Å / Num. obs: 21842 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 40.451 Å2 / Rmerge(I) obs: 0.133 / Net I/σ(I): 12.13
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
2.79-2.960.6940.5813.6419199349833600.64596.1
2.96-3.160.4470.3675.5919169328832850.40799.9
3.16-3.410.2990.2438.0717739305430470.2799.8
3.41-3.740.1970.15611.5316473284428400.17399.9
3.74-4.180.1310.10914.8214842258025740.12299.8
4.18-4.810.080.07719.0213068229422910.08599.9
4.81-5.880.0760.07319.5411039196219510.08199.4
5.88-8.240.0670.06520.528572155415510.07299.8
8.240.0370.04726.8247759569430.05298.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
BSSdata collection
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.79→43.67 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.876 / Occupancy max: 1 / Occupancy min: 1 / SU B: 14.525 / SU ML: 0.291 / Cross valid method: THROUGHOUT / ESU R Free: 0.418
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2588 1090 5 %RANDOM
Rwork0.2277 ---
obs0.2293 21842 99.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 111.34 Å2 / Biso mean: 30.7397 Å2 / Biso min: 5.9 Å2
Baniso -1Baniso -2Baniso -3
1-3.77 Å20 Å20 Å2
2---2.4 Å20 Å2
3----1.37 Å2
Refinement stepCycle: LAST / Resolution: 2.79→43.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6583 0 62 35 6680
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.026840
X-RAY DIFFRACTIONr_bond_other_d0.0040.024598
X-RAY DIFFRACTIONr_angle_refined_deg1.7651.9559328
X-RAY DIFFRACTIONr_angle_other_deg3.175311118
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1875823
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.89423.197319
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.977151047
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9121546
X-RAY DIFFRACTIONr_chiral_restr0.0890.21020
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217600
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021491
LS refinement shellResolution: 2.79→2.864 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 64 -
Rwork0.323 1295 -
all-1359 -
obs-1295 91.21 %

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