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- PDB-2xr4: C-terminal domain of BC2L-C Lectin from Burkholderia cenocepacia -

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Basic information

Entry
Database: PDB / ID: 2xr4
TitleC-terminal domain of BC2L-C Lectin from Burkholderia cenocepacia
ComponentsLECTIN
KeywordsSUGAR BINDING PROTEIN / LUNG / PATHOGEN
Function / homology
Function and homology information


identical protein binding
Similarity search - Function
Lectin Bc2l-C, N-terminal / : / Bc2l-C, N-terminal domain / Calcium-mediated lectin / Calcium-mediated lectin / Calcium-mediated lectin superfamily / Fucose-binding lectin II (PA-IIL) / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesBURKHOLDERIA CENOCEPACIA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSulak, O. / Cioci, G. / Lameignere, E. / Delia, M. / Wimmerova, M. / Imberty, A.
CitationJournal: Plos Pathog. / Year: 2011
Title: Burkholderia Cenocepacia Bc2L-C is a Super Lectin with Dual Specificity and Proinflammatory Activity.
Authors: Sulak, O. / Cioci, G. / Lameignere, E. / Balloy, V. / Round, A. / Gutsche, I. / Malinovska, L. / Chignard, M. / Kosma, P. / Aubert, D.F. / Marolda, C.L. / Valvano, M.A. / Wimmerova, M. / Imberty, A.
History
DepositionSep 9, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2011Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: LECTIN
B: LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3564
Polymers25,1642
Non-polymers1922
Water5,152286
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-41.7 kcal/mol
Surface area10280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.814, 100.814, 47.313
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein LECTIN / MANNOSE BINDING LECTIN / BC2L-C C-TERMINAL DOMAIN


Mass: 12581.974 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BURKHOLDERIA CENOCEPACIA (bacteria) / Strain: J2315 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: B4EH86
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.8 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal growpH: 5.5
Details: 100 MM SODIUM CITRATE PH 5.5, 2.5 M AMMONIUM SULPHATE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Details: MIRRORS
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 0.93→40 Å / Num. obs: 21834 / % possible obs: 97.5 % / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Biso Wilson estimate: 27.2 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 11.3
Reflection shellResolution: 1.9→2 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.02 / Mean I/σ(I) obs: 2.8 / % possible all: 86

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BV4

2bv4


Resolution: 1.9→87.37 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.504 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.19938 1094 5.1 %RANDOM
Rwork0.15562 ---
obs0.15781 20177 97.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.501 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å2-0.2 Å20 Å2
2---0.39 Å20 Å2
3---0.59 Å2
Refinement stepCycle: LAST / Resolution: 1.9→87.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1754 0 10 286 2050
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221846
X-RAY DIFFRACTIONr_bond_other_d0.0020.021223
X-RAY DIFFRACTIONr_angle_refined_deg1.4751.9542517
X-RAY DIFFRACTIONr_angle_other_deg0.84732989
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8825244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.18324.94591
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.43415285
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8471511
X-RAY DIFFRACTIONr_chiral_restr0.0890.2272
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212140
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02373
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_it0.9861.51169
X-RAY DIFFRACTIONr_mcbond_other0.2341.5487
X-RAY DIFFRACTIONr_mcangle_it1.79221879
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5173677
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.1334.5633
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 63 -
Rwork0.222 1262 -
obs--81.69 %

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