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- PDB-3vmp: Crystal structure of dextranase from Streptococcus mutans in comp... -

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Basic information

Entry
Database: PDB / ID: 3vmp
TitleCrystal structure of dextranase from Streptococcus mutans in complex with 4,5-epoxypentyl alpha-D-glucopyranoside
ComponentsDextranase
KeywordsHYDROLASE / TIM Barrel / immunoglobrin fold / Greek-key motif / Glycoside hydrolase family 66
Function / homology
Function and homology information


dextranase / dextranase activity / extracellular region / membrane
Similarity search - Function
Glycosyl hydrolase family 66 / Glycosyl hydrolase family 66 / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Immunoglobulins / TIM Barrel ...Glycosyl hydrolase family 66 / Glycosyl hydrolase family 66 / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
5-hydroxypentyl alpha-D-glucopyranoside / PHOSPHATE ION / Dextranase / Dextranase
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsSuzuki, N. / Fujimoto, Z. / Kim, Y.M. / Momma, M. / Okuyama, M. / Mori, H. / Funane, K. / Kimura, A.
Citation
Journal: J.Biol.Chem. / Year: 2012
Title: Structural elucidation of dextran degradation mechanism by streptococcus mutans dextranase belonging to glycoside hydrolase family 66
Authors: Suzuki, N. / Kim, Y.M. / Fujimoto, Z. / Momma, M. / Okuyama, M. / Mori, H. / Funane, K. / Kimura, A.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Crystallization and preliminary crystallographic analysis of dextranase from Streptococcus mutans.
Authors: Suzuki, N. / Kim, Y.M. / Fujimoto, Z. / Momma, M. / Kang, H.K. / Funane, K. / Okuyama, M. / Mori, H. / Kimura, A.
History
DepositionDec 14, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references / Derived calculations
Category: chem_comp / pdbx_chem_comp_identifier ...chem_comp / pdbx_chem_comp_identifier / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dextranase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,9583
Polymers72,5961
Non-polymers3612
Water6,720373
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.428, 89.966, 62.842
Angle α, β, γ (deg.)90.00, 102.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Dextranase


Mass: 72596.383 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 100-732
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: ATCC 25175 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: F5BA50, UniProt: Q54443*PLUS, dextranase
#2: Sugar ChemComp-E5G / 5-hydroxypentyl alpha-D-glucopyranoside / 5-hydroxypentyl alpha-D-glucoside / 5-hydroxypentyl D-glucoside / 5-hydroxypentyl glucoside


Type: D-saccharide / Mass: 266.288 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C11H22O7
IdentifierTypeProgram
5-hydroxypentyl-a-D-glucopyranosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / 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: 2.03 Å3/Da / Density % sol: 39.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 30% PEGMME 2000, 0.1M phosphate-citrate, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 10, 2008
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.88→61.41 Å / Num. obs: 45454 / % possible obs: 98.3 % / Redundancy: 6.9 % / Biso Wilson estimate: 29.4 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 28.9
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.267 / Mean I/σ(I) obs: 5.4 / Num. unique all: 4112 / % possible all: 89.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VMN

3vmn


Resolution: 1.88→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.851 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23771 2306 5.1 %RANDOM
Rwork0.19548 ---
obs0.19762 43068 96.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.537 Å2
Baniso -1Baniso -2Baniso -3
1-3.57 Å20 Å20.42 Å2
2---0.93 Å20 Å2
3----2.47 Å2
Refinement stepCycle: LAST / Resolution: 1.88→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5012 0 23 373 5408
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0225140
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5381.9476994
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8095631
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.23225.763262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.29815847
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2951519
X-RAY DIFFRACTIONr_chiral_restr0.1140.2767
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213969
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9071.53144
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.59125063
X-RAY DIFFRACTIONr_scbond_it2.51931996
X-RAY DIFFRACTIONr_scangle_it4.0294.51931
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.884→1.933 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 120 -
Rwork0.246 2247 -
obs--67.69 %

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