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- PDB-4xb3: Structure of dextran glucosidase -

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Basic information

Entry
Database: PDB / ID: 4xb3
TitleStructure of dextran glucosidase
ComponentsGlucan 1,6-alpha-glucosidase
KeywordsHYDROLASE / glycoside hydrolase / dextran glucosidase / intermediate
Function / homology
Function and homology information


glucan 1,6-alpha-glucosidase / glucan 1,6-alpha-glucosidase activity / carbohydrate metabolic process / cytoplasm
Similarity search - Function
Glycosyl hydrolase, C-terminal (DUF3459) / Domain of unknown function (DUF3459) / 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 ...Glycosyl hydrolase, C-terminal (DUF3459) / Domain of unknown function (DUF3459) / 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
Glucan 1,6-alpha-glucosidase
Similarity search - Component
Biological speciesStreptococcus mutans UA159 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.093 Å
AuthorsKobayashi, M. / Kato, K. / Yao, M.
Funding support Japan, 2items
OrganizationGrant numberCountry
the Japan Society for the Promotion of Science24-871 Japan
the Ministry of Education, Culture, Sports, Science and Technology Japan
CitationJournal: Febs Lett. / Year: 2015
Title: Structural insights into the catalytic reaction that is involved in the reorientation of Trp238 at the substrate-binding site in GH13 dextran glucosidase
Authors: Kobayashi, M. / Saburi, W. / Nakatsuka, D. / Hondoh, H. / Kato, K. / Okuyama, M. / Mori, H. / Kimura, A. / Yao, M.
History
DepositionDec 16, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
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_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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucan 1,6-alpha-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5076
Polymers62,0651
Non-polymers4435
Water6,359353
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area20100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.151, 82.550, 103.559
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glucan 1,6-alpha-glucosidase / Dextran glucosidase / Exo-1 / 6-alpha-glucosidase / Glucodextranase


Mass: 62064.844 Da / Num. of mol.: 1 / Mutation: E236Q, N536L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans UA159 (bacteria) / Gene: dexB, SMU_883 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99040, glucan 1,6-alpha-glucosidase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 353 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 100mM Sodium HEPES, 200mM CaCl2, 180mg/ml PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 36936 / % possible obs: 99.4 % / Redundancy: 5.84 % / Rsym value: 0.088 / Net I/σ(I): 14.81
Reflection shellResolution: 2.09→2.22 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 4.45 / % possible all: 97.4

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementResolution: 2.093→48.108 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.219 1840 4.98 %
Rwork0.1794 --
obs0.1813 36931 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.093→48.108 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4373 0 23 353 4749
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034507
X-RAY DIFFRACTIONf_angle_d0.7046108
X-RAY DIFFRACTIONf_dihedral_angle_d12.611654
X-RAY DIFFRACTIONf_chiral_restr0.029637
X-RAY DIFFRACTIONf_plane_restr0.003788
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0934-2.150.26741400.2372538X-RAY DIFFRACTION95
2.15-2.21330.23211250.20342673X-RAY DIFFRACTION100
2.2133-2.28470.21571620.19012676X-RAY DIFFRACTION100
2.2847-2.36640.26211440.18682658X-RAY DIFFRACTION100
2.3664-2.46110.25521390.19152672X-RAY DIFFRACTION100
2.4611-2.57310.23921470.19312689X-RAY DIFFRACTION100
2.5731-2.70880.28281340.20082664X-RAY DIFFRACTION100
2.7088-2.87850.27131520.19482719X-RAY DIFFRACTION100
2.8785-3.10070.22291290.19792693X-RAY DIFFRACTION100
3.1007-3.41260.19671270.18482739X-RAY DIFFRACTION100
3.4126-3.90630.21991570.16332707X-RAY DIFFRACTION100
3.9063-4.92070.151320.14362768X-RAY DIFFRACTION99
4.9207-48.12050.20831520.16572895X-RAY DIFFRACTION100

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