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- PDB-1ulv: Crystal Structure of Glucodextranase Complexed with Acarbose -

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Basic information

Entry
Database: PDB / ID: 1ulv
TitleCrystal Structure of Glucodextranase Complexed with Acarbose
Componentsglucodextranase
KeywordsHYDROLASE / GH family 15 / (alpha-alpha)6-barrel / SLH domain
Function / homology
Function and homology information


glucan 1,4-alpha-glucosidase activity / carbohydrate binding / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Glucodextranase, domain B / Glucodextranase-like, C-terminal / C-terminal binding-module, SLH-like, of glucodextranase / Glucoamylase, bacterial / Glucodextranase, N-terminal / Glucodextranase, domain N / Immunoglobulin-like - #1190 / : / Glucoamylase active site region signature. / GH15-like domain ...Glucodextranase, domain B / Glucodextranase-like, C-terminal / C-terminal binding-module, SLH-like, of glucodextranase / Glucoamylase, bacterial / Glucodextranase, N-terminal / Glucodextranase, domain N / Immunoglobulin-like - #1190 / : / Glucoamylase active site region signature. / GH15-like domain / Glycosyl hydrolases family 15 / Beta-galactosidase; Chain A, domain 5 - #10 / Glycosyltransferase - #10 / Glycoside hydrolase-type carbohydrate-binding / Beta-galactosidase; Chain A, domain 5 / Galactose mutarotase-like domain superfamily / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Distorted Sandwich / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
acarbose-derived trisaccharide / Glucodextranase
Similarity search - Component
Biological speciesArthrobacter globiformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsMizuno, M. / Tonozuka, T. / Suzuki, S. / Uotsu-Tomita, R. / Kamitori, S. / Nishikawa, A. / Sakano, Y.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structural insights into substrate specificity and function of glucodextranase
Authors: Mizuno, M. / Tonozuka, T. / Suzuki, S. / Uotsu-Tomita, R. / Kamitori, S. / Nishikawa, A. / Sakano, Y.
History
DepositionSep 16, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type / 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_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
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: glucodextranase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,2518
Polymers106,5271
Non-polymers7247
Water7,855436
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)198.795, 88.247, 80.994
Angle α, β, γ (deg.)90.00, 112.55, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein glucodextranase


Mass: 106526.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arthrobacter globiformis (bacteria) / Strain: I42 / References: UniProt: Q9LBQ9, glucan 1,6-alpha-glucosidase
#2: 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 / acarbose-derived trisaccharide


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 483.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: acarbose-derived trisaccharide
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2122m-1a_1-5_4*NC^SC^SC^SC^RCCO/7=^ZC$3/6O/5O/4O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp]{[(4+1)][a-D-6-deoxy-Glcp4N]{[(4+1)][<C7O4>]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 436 / 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: 2.94 Å3/Da / Density % sol: 57.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.1
Details: PEG 8000, potassium dihydrogen phosphate, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18 mg/mlprotein1drop
220 mMsodium acetate1droppH6.0
35 mMcalcium acetate1drop
43.0 %(w/v)PEG80001reservoir
580 mMpotassium dihydrogen phosphate1reservoir
650 mMsodium acetate1reservoirpH5.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 28, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.418→49.59 Å / Num. all: 48692 / Num. obs: 48692 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 23 Å2
Reflection shellResolution: 2.42→2.51 Å / % possible all: 95.3
Reflection
*PLUS
Highest resolution: 2.42 Å / Lowest resolution: 49.4 Å / Num. measured all: 184944 / Rmerge(I) obs: 0.069
Reflection shell
*PLUS
% possible obs: 95.3 % / Rmerge(I) obs: 0.206

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.42→49.59 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 4504609.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.238 4919 10.1 %RANDOM
Rwork0.196 ---
obs0.196 48692 98 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.1101 Å2 / ksol: 0.371971 e/Å3
Displacement parametersBiso mean: 26.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.7 Å20 Å26.05 Å2
2---4.14 Å20 Å2
3---5.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.42→49.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7506 0 38 436 7980
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.171.5
X-RAY DIFFRACTIONc_mcangle_it1.872
X-RAY DIFFRACTIONc_scbond_it1.952
X-RAY DIFFRACTIONc_scangle_it2.722.5
LS refinement shellResolution: 2.42→2.55 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.286 689 10.3 %
Rwork0.225 5994 -
obs--79.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5ACR.PARAMACR.TOP
Refinement
*PLUS
Lowest resolution: 49.6 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77
LS refinement shell
*PLUS
Lowest resolution: 2.51 Å

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