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- PDB-6htv: Crystal structure of Leuconostoc citreum NRRL B-1299 N-terminally... -

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Basic information

Entry
Database: PDB / ID: 6htv
TitleCrystal structure of Leuconostoc citreum NRRL B-1299 N-terminally truncated dextransucrase DSR-M in complex with isomaltotetraose
ComponentsAlternansucrase
KeywordsTRANSFERASE / dextransucrase / dextran
Function / homology
Function and homology information


dextransucrase activity / dextransucrase / glucan biosynthetic process / glucosyltransferase activity / metal ion binding
Similarity search - Function
Glycoside hydrolase, family 70, catalytic domain / Glycosyl hydrolase family 70 / Choline-binding repeat / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesLeuconostoc citreum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9 Å
AuthorsClaverie, M. / Cioci, G. / Remaud-Simeon, M. / Moulis, C. / Lippens, G.
CitationJournal: Biochemistry / Year: 2019
Title: Futile Encounter Engineering of the DSR-M Dextransucrase Modifies the Resulting Polymer Length.
Authors: Claverie, M. / Cioci, G. / Guionnet, M. / Schorghuber, J. / Lichtenecker, R. / Moulis, C. / Remaud-Simeon, M. / Lippens, G.
History
DepositionOct 4, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alternansucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,6833
Polymers143,9761
Non-polymers7072
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint1 kcal/mol
Surface area42740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.308, 185.308, 150.774
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Alternansucrase / DSR-M glucansucrase inactive mutant E715Q


Mass: 143976.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leuconostoc citreum (bacteria) / Gene: asr / Plasmid: pet55 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: A0A2H4A2Q1, EC: 2.4.1.140
#2: Polysaccharide alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1a_1-5]/1-1-1-1/a6-b1_b6-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(6+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{[(6+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

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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: 4.98 Å3/Da / Density % sol: 75 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 3350 20 %, 0.2 M Sodium citrate tribasic dihydrate, 0.1 M Bis-Tris propane 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 3.9→47.96 Å / Num. obs: 26662 / % possible obs: 97.3 % / Redundancy: 4.7 % / Net I/σ(I): 13.5
Reflection shellResolution: 3.9→4.11 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LFC

5lfc


Resolution: 3.9→47.96 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.906 / SU B: 32.498 / SU ML: 0.423 / Cross valid method: THROUGHOUT / ESU R Free: 0.537 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23209 1319 4.9 %RANDOM
Rwork0.21015 ---
obs0.21125 25343 96.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 115.304 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20.06 Å2-0 Å2
2--0.11 Å20 Å2
3----0.36 Å2
Refinement stepCycle: 1 / Resolution: 3.9→47.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8362 0 46 0 8408
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.028591
X-RAY DIFFRACTIONr_bond_other_d0.0010.027739
X-RAY DIFFRACTIONr_angle_refined_deg1.3691.93911686
X-RAY DIFFRACTIONr_angle_other_deg0.954317795
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.78551063
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.4625.701442
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.679151378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5641529
X-RAY DIFFRACTIONr_chiral_restr0.0810.21277
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210072
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022047
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_it6.46311.4284255
X-RAY DIFFRACTIONr_mcbond_other6.45711.4284254
X-RAY DIFFRACTIONr_mcangle_it10.02517.1495317
X-RAY DIFFRACTIONr_mcangle_other10.02417.155318
X-RAY DIFFRACTIONr_scbond_it6.98111.854336
X-RAY DIFFRACTIONr_scbond_other6.98111.854336
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.93817.5996370
X-RAY DIFFRACTIONr_long_range_B_refined15.76636612
X-RAY DIFFRACTIONr_long_range_B_other15.76336610
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.9→4.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 76 -
Rwork0.295 1851 -
obs--95.4 %

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