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- PDB-3wy1: Crystal structure of alpha-glucosidase -

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Basic information

Entry
Database: PDB / ID: 3wy1
TitleCrystal structure of alpha-glucosidase
ComponentsAlpha-glucosidase
KeywordsHYDROLASE / alpha-glucosidase / TIM barrel / glucosidase / Carbohydrate/Sugar Binding
Function / homology
Function and homology information


: / alpha-glucosidase / oligosaccharide catabolic process / alpha-amylase activity / metal ion binding
Similarity search - Function
Maltogenic Amylase, C-terminal / Maltogenic Amylase, C-terminal domain / Oligo-1,6-glucosidase; domain 2 / Oligo-1,6-glucosidase; Domain 2 / Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta ...Maltogenic Amylase, C-terminal / Maltogenic Amylase, C-terminal domain / Oligo-1,6-glucosidase; domain 2 / Oligo-1,6-glucosidase; Domain 2 / Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
(3R,5R,7R)-octane-1,3,5,7-tetracarboxylic acid / Alpha-glucosidase
Similarity search - Component
Biological speciesHalomonas sp. H11 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsShen, X. / Gai, Z. / Kato, K. / Yao, M.
CitationJournal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2015
Title: Structural analysis of the alpha-glucosidase HaG provides new insights into substrate specificity and catalytic mechanism
Authors: Shen, X. / Saburi, W. / Gai, Z. / Kato, K. / Ojima-Kato, T. / Yu, J. / Komoda, K. / Kido, Y. / Matsui, H. / Mori, H. / Yao, M.
History
DepositionAug 18, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Mar 21, 2018Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-glucosidase
B: Alpha-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,0757
Polymers122,3542
Non-polymers7215
Water11,692649
1
A: Alpha-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5844
Polymers61,1771
Non-polymers4073
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4923
Polymers61,1771
Non-polymers3152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.540, 119.590, 177.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: ALA / End label comp-ID: ALA / Auth seq-ID: 4 - 538 / Label seq-ID: 4 - 538

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

#1: Protein Alpha-glucosidase


Mass: 61177.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halomonas sp. H11 (bacteria) / Gene: aglA / Plasmid: pFLAG-CTS / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H3K096, alpha-glucosidase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PRU / (3R,5R,7R)-octane-1,3,5,7-tetracarboxylic acid / Polyacrylic acid


Mass: 290.267 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H18O8
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 649 / 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: 2.63 Å3/Da / Density % sol: 53.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% Polyacrylic acid 5100 sodium salt, 0.1M HEPES, 0.02M magnesium chloride, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 23, 2013 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→99.3 Å / Num. all: 71435 / Num. obs: 71192 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 35.3 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 20.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.15-2.287.40.4895.7511231198.7
2.28-2.437.40.3378.0710723199.9
2.43-2.637.40.24610.499993199.9
2.63-2.887.40.15514.9392111100
2.88-3.227.30.09521.98382199.9
3.22-3.717.20.05432.717430199.9
3.71-4.5470.03943.326311199.7
4.54-6.3970.03446.924983199.7
6.39-99.36.80.02852.822928199.1

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
PHENIX(phenix.refine: dev_1391)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M53

1m53


Resolution: 2.15→44.493 Å / FOM work R set: 0.8083 / SU ML: 0.21 / σ(F): 1.36 / Phase error: 25.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2194 3552 5 %RANDOM
Rwork0.1825 ---
all0.1844 71435 --
obs0.1844 71076 99.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.45 Å2 / Biso mean: 35.4 Å2 / Biso min: 16.96 Å2
Refinement stepCycle: LAST / Resolution: 2.15→44.493 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8584 0 48 649 9281
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088889
X-RAY DIFFRACTIONf_angle_d1.13112121
X-RAY DIFFRACTIONf_chiral_restr0.0761258
X-RAY DIFFRACTIONf_plane_restr0.0051614
X-RAY DIFFRACTIONf_dihedral_angle_d12.9793206
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5105X-RAY DIFFRACTION5.495TORSIONAL
12B5105X-RAY DIFFRACTION5.495TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.15-2.17950.30141410.269226882829100
2.1795-2.21060.28611400.245826492789100
2.2106-2.24360.26591420.253226912833100
2.2436-2.27860.28821380.228426272765100
2.2786-2.3160.29411410.234226792820100
2.316-2.35590.26451400.214726572797100
2.3559-2.39880.29061410.224326872828100
2.3988-2.44490.25851410.206226762817100
2.4449-2.49480.25441390.219426522791100
2.4948-2.5490.2791410.211226812822100
2.549-2.60830.26471400.202326702810100
2.6083-2.67360.23091420.20426842826100
2.6736-2.74580.25191420.193726952837100
2.7458-2.82660.24661400.205226692809100
2.8266-2.91780.26451420.199627042846100
2.9178-3.02210.22941420.203626952837100
3.0221-3.14310.23781420.200626952837100
3.1431-3.28610.2351420.190226972839100
3.2861-3.45930.21421420.184927142856100
3.4593-3.67590.18571420.170726992841100
3.6759-3.95960.18491440.158227382882100
3.9596-4.35770.17881440.138427362880100
4.3577-4.98760.15331450.13462749289499
4.9876-6.2810.18581460.150327742920100
6.281-44.5020.18571530.16432918307199

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