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- PDB-2zic: Crystal structure of Streptococcus mutans dextran glucosidase -

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Basic information

Entry
Database: PDB / ID: 2zic
TitleCrystal structure of Streptococcus mutans dextran glucosidase
ComponentsDextran glucosidase
KeywordsHYDROLASE / TIM barrel / (beta/alpha)8-barrel
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
Dextran glucosidase / Glucan 1,6-alpha-glucosidase
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHondoh, H. / Saburi, W. / Mori, H. / Okuyama, M. / Nakada, T. / Matsuura, Y. / Kimura, A.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Substrate recognition mechanism of alpha-1,6-glucosidic linkage hydrolyzing enzyme, dextran glucosidase from Streptococcus mutans.
Authors: Hondoh, H. / Saburi, W. / Mori, H. / Okuyama, M. / Nakada, T. / Matsuura, Y. / Kimura, A.
History
DepositionFeb 14, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 24, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dextran glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3586
Polymers63,0241
Non-polymers3345
Water7,296405
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.720, 86.470, 104.300
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 Dextran glucosidase


Mass: 63023.840 Da / Num. of mol.: 1 / Mutation: N536L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Gene: dexB / Plasmid: pET-23d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CodonPlus RIL
References: UniProt: Q2HWU5, UniProt: Q99040*PLUS, glucan 1,6-alpha-glucosidase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 405 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF THE RESIDUES 1-5 IS DESIGNED ACCORDING TO THE SEQUENCE OF THE RESIDUES 1-5 REPORTED ...THE SEQUENCE OF THE RESIDUES 1-5 IS DESIGNED ACCORDING TO THE SEQUENCE OF THE RESIDUES 1-5 REPORTED IN UNIPLOT Q99040, DEXB_STRMU (DEXTRAN GLUCOSIDASE FROM STREPTOCOCCUS MUTANS UA159)

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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: 2.6 Å3/Da / Density % sol: 52.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM tris-HCl, 12% PEG6000, 200mM NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 12, 2005
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→36 Å / Num. obs: 32892 / % possible obs: 96.8 % / Biso Wilson estimate: 12.8 Å2

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Processing

Software
NameVersionClassification
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UOK

1uok


Resolution: 2.2→9.99 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1929024.74 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1605 5 %RANDOM
Rwork0.183 ---
obs0.183 32288 95.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.7635 Å2 / ksol: 0.45 e/Å3
Displacement parametersBiso mean: 15.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.85 Å20 Å20 Å2
2--6.56 Å20 Å2
3----4.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 2.2→9.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4373 0 17 405 4795
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.77
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.229 246 5.1 %
Rwork0.185 4561 -
obs--87.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water.paramwater.top
X-RAY DIFFRACTION4lig2.paramlig2.top

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