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- PDB-5ngy: Crystal structure of Leuconostoc citreum NRRL B-1299 dextransucra... -

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Basic information

Entry
Database: PDB / ID: 5ngy
TitleCrystal structure of Leuconostoc citreum NRRL B-1299 dextransucrase DSR-M
ComponentsDSR-M glucansucrase inactive mutant E715Q
KeywordsTRANSFERASE / dextransucrase / dextran / sugar binding protein
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
PRASEODYMIUM ION / dextransucrase
Similarity search - Component
Biological speciesLeuconostoc citreum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsClaverie, M. / Cioci, G. / Remaud-simeon, M. / Moulis, C. / Tranier, S. / Vuillemin, M.
CitationJournal: Acs Catalysis / Year: 2017
Title: Investigations on the Determinants Responsible for Low Molar Mass Dextran Formation by DSR-M Dextransucrase
Authors: Claverie, M. / Cioci, G. / Vuillemin, M. / Monties, N. / Roblin, P. / Lippens, G. / Remaud-simeon, M. / Moulis, C.
History
DepositionMar 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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.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.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _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 17, 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 / struct_ncs_dom_lim
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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DSR-M glucansucrase inactive mutant E715Q
B: DSR-M glucansucrase inactive mutant E715Q
hetero molecules


Theoretical massNumber of molelcules
Total (without water)289,54511
Polymers287,9532
Non-polymers1,5929
Water00
1
A: DSR-M glucansucrase inactive mutant E715Q
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,1066
Polymers143,9761
Non-polymers1,1295
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DSR-M glucansucrase inactive mutant E715Q
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,4395
Polymers143,9761
Non-polymers4634
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.869, 128.810, 234.518
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNSERSERAA290 - 494127 - 331
21ASNASNSERSERBB290 - 494127 - 331
12LEULEULYSLYSAA496 - 1434333 - 1271
22LEULEULYSLYSBB496 - 1434333 - 1271

NCS ensembles :
ID
1
2

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Components

#1: Protein DSR-M glucansucrase inactive mutant E715Q


Mass: 143976.469 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leuconostoc citreum (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2H4A2Q1*PLUS
#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.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-PR / PRASEODYMIUM ION


Mass: 140.908 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: Pr

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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: 2.78 Å3/Da / Density % sol: 55.7 % / Description: thin rod
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG3350, 0.2M KSCN, 0.1 Pr(III)acetate, BIS-TRIS pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 15, 2016 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 3.7→50 Å / Num. obs: 34388 / % possible obs: 98.3 % / Redundancy: 4.3 % / Biso Wilson estimate: 44.5 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.195 / Rpim(I) all: 0.1 / Net I/σ(I): 3.6
Reflection shellResolution: 3.7→3.9 Å / Redundancy: 4 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4910 / CC1/2: 0.822 / Rpim(I) all: 0.284 / % possible all: 97.3

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Processing

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

5lfc


Resolution: 3.7→50 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.866 / SU B: 80.89 / SU ML: 0.517 / Cross valid method: THROUGHOUT / ESU R Free: 0.681 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23643 1693 4.9 %RANDOM
Rwork0.19234 ---
obs0.19453 32648 98.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.15 Å2
Baniso -1Baniso -2Baniso -3
1--5.87 Å20 Å2-0 Å2
2--0.14 Å20 Å2
3---5.74 Å2
Refinement stepCycle: 1 / Resolution: 3.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18805 0 53 0 18858
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0219264
X-RAY DIFFRACTIONr_bond_other_d0.0030.0217262
X-RAY DIFFRACTIONr_angle_refined_deg1.0981.93326188
X-RAY DIFFRACTIONr_angle_other_deg0.83339636
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.84552405
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.56225.619993
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.266153027
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2081562
X-RAY DIFFRACTIONr_chiral_restr0.0690.22828
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0222765
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024671
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_it1.3464.7999628
X-RAY DIFFRACTIONr_mcbond_other1.3464.7999627
X-RAY DIFFRACTIONr_mcangle_it2.2677.212025
X-RAY DIFFRACTIONr_mcangle_other2.2677.212026
X-RAY DIFFRACTIONr_scbond_it1.2884.8819636
X-RAY DIFFRACTIONr_scbond_other1.2884.8819636
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2427.28414164
X-RAY DIFFRACTIONr_long_range_B_refined3.47638.1121414
X-RAY DIFFRACTIONr_long_range_B_other3.47638.11221415
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A93570.12
12B93570.12
21A542550.07
22B542550.07
LS refinement shellResolution: 3.7→3.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 112 -
Rwork0.263 2375 -
obs--97.41 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8361-0.0324-0.20430.16290.04170.22950.01010.14430.0415-0.0918-0.01880.0516-0.0852-0.06370.00870.11130.0037-0.02160.036-0.00280.0232-34.560916.8137-26.6144
20.5182-0.0439-0.38790.388-0.12350.7111-0.03420.02860.00930.09230.005-0.1268-0.0532-0.13790.02920.14790.0412-0.02980.04740.00150.0422-23.8901-14.456428.0412
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A171 - 1501
2X-RAY DIFFRACTION2B290 - 1501

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