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- PDB-2wra: BclA lectin from Burkholderia cenocepacia complexed with aMan1(aM... -

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Basic information

Entry
Database: PDB / ID: 2wra
TitleBclA lectin from Burkholderia cenocepacia complexed with aMan1(aMan1- 6)-3Man trisaccharide
ComponentsLECTIN
KeywordsSUGAR BINDING PROTEIN / BACTERIAL LECTIN / OLIGOSACCHARIDES
Function / homologyCalcium-mediated lectin / Calcium-mediated lectin / Calcium-mediated lectin superfamily / Fucose-binding lectin II (PA-IIL) / Jelly Rolls / Sandwich / Mainly Beta / metal ion binding / Lectin
Function and homology information
Biological speciesBURKHOLDERIA CENOCEPACIA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsLameignere, E. / Shiao, T.C. / Roy, R. / Wimmerova, M. / Dubreuil, F. / Varrot, A. / Imberty, A.
CitationJournal: Glycobiology / Year: 2010
Title: Structural Basis of the Affinity for Oligomannosides and Analogs Displayed by Bc2L-A, a Burkholderia Cenocepacia Soluble Lectin.
Authors: Lameignere, E. / Shiao, T.C. / Roy, R. / Wimmerova, M. / Dubreuil, F. / Varrot, A. / Imberty, A.
History
DepositionSep 1, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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 / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: 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_sheet
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands
Remark 650 HELIX DETERMINATION METHOD: PROVIDED BY DEPOSITOR
Remark 700 SHEET DETERMINATION METHOD: PROVIDED BY DEPOSITOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4605
Polymers13,7791
Non-polymers6814
Water3,207178
1
A: LECTIN
hetero molecules

A: LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,91910
Polymers27,5582
Non-polymers1,3618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area3100 Å2
ΔGint-40.23 kcal/mol
Surface area10840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.296, 66.296, 46.159
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-2061-

HOH

21A-2164-

HOH

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Components

#1: Protein LECTIN / BCLA


Mass: 13779.034 Da / Num. of mol.: 1 / Fragment: BCLA MONOMER, RESIDUES 2-129
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BURKHOLDERIA CENOCEPACIA (bacteria) / Strain: J2315
Description: DNA FROM BURKHOLDERIA CENOCEPACIA STRAIN J2315 OBTAINED FROM THE CZECH COLLECTION OF MICROORGANISMS AT BRNO
Plasmid: PRSET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B4EH87
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a1122h-1a_1-5]/1-1-1/a3-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsALPHA-D-MANNOSE (MAN): AMAN1-3AMAN1-6MAN TRISACCHARIDE

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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: 2.13 Å3/Da / Density % sol: 42.17 % / Description: NONE
Crystal growDetails: 80% OF THE INITIAL PRECIPITANT SOLUTION (30% PEG IN 0.2M AMMONIUM SULPHATE)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9794999
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 18, 2006 / Details: MIRRORS
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794999 Å / Relative weight: 1
ReflectionResolution: 1.1→57.45 Å / Num. obs: 47704 / % possible obs: 96.5 % / Observed criterion σ(I): 2.4 / Redundancy: 4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.8
Reflection shellResolution: 1.1→1.16 Å / Redundancy: 2 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 2.4 / % possible all: 79.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VNV

2vnv


Resolution: 1.1→57.45 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.965 / SU B: 0.819 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.031 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.173 2303 5 %RANDOM
Rwork0.14355 ---
obs0.14499 43671 96.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.224 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20.06 Å20 Å2
2--0.12 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.1→57.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms932 0 41 178 1151
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221069
X-RAY DIFFRACTIONr_bond_other_d0.0010.02713
X-RAY DIFFRACTIONr_angle_refined_deg2.011.9831468
X-RAY DIFFRACTIONr_angle_other_deg1.55131738
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0185138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.93524.650
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.6115158
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.552156
X-RAY DIFFRACTIONr_chiral_restr0.1340.2167
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211210
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02215
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_it1.9021.5656
X-RAY DIFFRACTIONr_mcbond_other0.8161.5266
X-RAY DIFFRACTIONr_mcangle_it2.85121064
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3793413
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.564.5401
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.65531782
X-RAY DIFFRACTIONr_sphericity_free9.6163180
X-RAY DIFFRACTIONr_sphericity_bonded4.12631751
LS refinement shellResolution: 1.101→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 115 -
Rwork0.317 2383 -
obs--72.41 %

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