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- PDB-3kll: Crystal structure of Lactobacillus reuteri N-terminally truncated... -

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Basic information

Entry
Database: PDB / ID: 3kll
TitleCrystal structure of Lactobacillus reuteri N-terminally truncated glucansucrase GTF180-maltose complex
ComponentsGlucansucrase
KeywordsTRANSFERASE / glucansucrase-maltose complex / multidomain protein / Glycosyltransferase
Function / homology
Function and homology information


dextransucrase activity / dextransucrase / glucan biosynthetic process / glucosyltransferase activity / metal ion binding
Similarity search - Function
Glucansucrase / Glycoside hydrolase, family 70, catalytic domain / Glycosyl hydrolase family 70 / Cholin Binding / left handed beta-beta-3-solenoid / KxYKxGKxW signal peptide / KxYKxGKxW signal peptide / Choline-binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. ...Glucansucrase / Glycoside hydrolase, family 70, catalytic domain / Glycosyl hydrolase family 70 / Cholin Binding / left handed beta-beta-3-solenoid / KxYKxGKxW signal peptide / KxYKxGKxW signal peptide / Choline-binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Ribbon / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / dextransucrase
Similarity search - Component
Biological speciesLactobacillus reuteri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsVujicic-Zagar, A. / Pijning, T. / Kralj, S. / Eeuwema, W. / Dijkhuizen, L. / Dijkstra, B.W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Crystal structure of a 117 kDa glucansucrase fragment provides insight into evolution and product specificity of GH70 enzymes
Authors: Vujicic-Zagar, A. / Pijning, T. / Kralj, S. / Lopez, C.A. / Eeuwema, W. / Dijkhuizen, L. / Dijkstra, B.W.
History
DepositionNov 8, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_source / 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 / struct_asym / struct_conn / struct_ref_seq_dif / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_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 / _diffrn_source.pdbx_synchrotron_site / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _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_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_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_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 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
Revision 2.2Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 2.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glucansucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,54510
Polymers117,7671
Non-polymers1,7789
Water13,655758
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.165, 65.850, 82.317
Angle α, β, γ (deg.)73.44, 78.57, 86.34
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Glucansucrase


Mass: 117767.336 Da / Num. of mol.: 1
Fragment: N-terminally truncated GTF180, UNP residues 742-1772
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus reuteri (bacteria) / Strain: 180 / Gene: gtf180 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5SBN3, dextransucrase
#2: Polysaccharide
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 758 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONFLICT F1674L MAY DUE TO PCR ERROR.

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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: 2.52 Å3/Da / Density % sol: 51.1 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 3350, BIS-TRIS propane buffer, CaCl2, pH 6.0, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.976 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 24, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.997→38.747 Å / Num. obs: 75992 / % possible obs: 97.5 % / Redundancy: 2.4 % / Rsym value: 0.053
Reflection shellResolution: 2→2.1 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 4.3 / Num. unique all: 10726 / Rsym value: 0.171 / % possible all: 94

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
PHASERphasing
REFMAC5.5.0088refinement
PDB_EXTRACT3.005data extraction
DNAdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KLK

3klk


Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0.8 / SU B: 3.576 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.164 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.199 3823 5 %RANDOM
Rwork0.163 ---
obs0.165 75815 97.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 233.6 Å2 / Biso mean: 29.568 Å2 / Biso min: 13.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å2-2.65 Å20.91 Å2
2--0.62 Å20.11 Å2
3----1.41 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7983 0 117 758 8858
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0228280
X-RAY DIFFRACTIONr_angle_refined_deg1.4031.94711260
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.24551006
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.97625.448435
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.16151307
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8471535
X-RAY DIFFRACTIONr_chiral_restr0.0990.21226
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216418
X-RAY DIFFRACTIONr_mcbond_it0.7751.54987
X-RAY DIFFRACTIONr_mcangle_it1.35128024
X-RAY DIFFRACTIONr_scbond_it2.20233289
X-RAY DIFFRACTIONr_scangle_it3.3044.53236
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 248 -
Rwork0.224 5218 -
all-5466 -
obs--96.2 %

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