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- PDB-3tto: Crystal structure of Leuconostoc mesenteroides NRRL B-1299 N-term... -

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Basic information

Entry
Database: PDB / ID: 3tto
TitleCrystal structure of Leuconostoc mesenteroides NRRL B-1299 N-terminally truncated dextransucrase DSR-E in triclinic form
ComponentsDextransucrase
KeywordsTRANSFERASE / (beta/alpha)8 barrel / sucrose/dextran/gluco-oligosaccharide binding / alpha-1 / 2 branching dextransucrase
Function / homology
Function and homology information


dextransucrase activity / dextransucrase / glucan biosynthetic process / glucosyltransferase activity / metal ion binding
Similarity search - Function
Glucan-binding repeat / 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 / Putative cell wall binding repeat ...Glucan-binding repeat / 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 / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / Glycosyl hydrolase, all-beta / Ribbon / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesLeuconostoc mesenteroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsBrison, Y. / Pijning, T. / Fabre, E. / Mourey, L. / Morel, S. / Potocki-Veronese, G. / Monsan, P. / Tranier, S. / Remaud-Simeon, M. / Dijkstra, B.W.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Functional and structural characterization of alpha-(1-2) branching sucrase derived from DSR-E glucansucrase
Authors: Brison, Y. / Pijning, T. / Malbert, Y. / Fabre, E. / Mourey, L. / Morel, S. / Potocki-Veronese, G. / Monsan, P. / Tranier, S. / Remaud-Simeon, M. / Dijkstra, B.W.
History
DepositionSep 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_asym_id / _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_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dextransucrase
B: Dextransucrase
C: Dextransucrase
D: Dextransucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)494,87317
Polymers493,8844
Non-polymers98913
Water59433
1
A: Dextransucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,6033
Polymers123,4711
Non-polymers1322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dextransucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,6954
Polymers123,4711
Non-polymers2243
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Dextransucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,7875
Polymers123,4711
Non-polymers3164
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Dextransucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,7875
Polymers123,4711
Non-polymers3164
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.840, 140.040, 155.460
Angle α, β, γ (deg.)85.36, 90.92, 76.85
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Dextransucrase


Mass: 123470.891 Da / Num. of mol.: 4
Fragment: N-terminally truncated DSR-E, UniProt residues 1759-2835
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leuconostoc mesenteroides (bacteria) / Strain: NRRL B-1299 / Gene: dsr-E, dsrE / Plasmid: pBAD Directional 102 (pBAD102) / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: Q8G9Q2, dextransucrase
#2: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.86 Å3/Da / Density % sol: 56.96 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 17% PEG 3350, 0.2 M ammonium iodide, 80 mM ammonium citrate, 2% glycerol, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 22, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 3.3→51.62 Å / Num. all: 82750 / Num. obs: 80648 / % possible obs: 97.5 % / Redundancy: 1.9 % / Biso Wilson estimate: 42.3 Å2 / Rsym value: 0.203 / Net I/σ(I): 4.1
Reflection shellResolution: 3.3→3.48 Å / Mean I/σ(I) obs: 1.6 / Rsym value: 0.533 / % possible all: 97

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.6.0117refinement
iMOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KLK

3klk


Resolution: 3.3→51.62 Å / Cor.coef. Fo:Fc: 0.858 / Cor.coef. Fo:Fc free: 0.758 / SU B: 33.4 / SU ML: 0.537 / Cross valid method: THROUGHOUT / ESU R Free: 0.642 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29075 4029 5 %RANDOM
Rwork0.22403 ---
obs0.2274 80648 97.46 %-
all-82716 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.267 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0.08 Å20.01 Å2
2--0 Å2-0.05 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 3.3→51.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32238 0 58 33 32329
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0233022
X-RAY DIFFRACTIONr_bond_other_d0.0010.0220620
X-RAY DIFFRACTIONr_angle_refined_deg1.1071.92245019
X-RAY DIFFRACTIONr_angle_other_deg0.827350327
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.40254205
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.74525.5171691
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.247154817
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8881599
X-RAY DIFFRACTIONr_chiral_restr0.0590.24907
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0238399
X-RAY DIFFRACTIONr_gen_planes_other0.0010.026824
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.3→3.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 260 -
Rwork0.315 5605 -
obs-5605 96.97 %

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