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- PDB-3zw2: Structure of the lectin Bambl from Burkholderia ambifaria in comp... -

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Basic information

Entry
Database: PDB / ID: 3zw2
TitleStructure of the lectin Bambl from Burkholderia ambifaria in complex with blood group H type 1 tetrasaccharide
ComponentsBAMBL LECTIN
KeywordsSUGAR BINDING PROTEIN / CYSTIC FIBROSIS / B-PROPELLER / HUMAN HISTO-BLOOD GROUP
Function / homologyLipocalin - #190 / Fucose-specific lectin / Fungal fucose-specific lectin / Lipocalin / Beta Barrel / Mainly Beta / H type 1 antigen, beta anomer / Fucose-binding lectin protein
Function and homology information
Biological speciesBURKHOLDERIA AMBIFARIA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsAudfray, A. / Claudinon, J. / Abounit, S. / Ruvoen-Clouet, N. / Larson, G. / Wimmerova, M. / Lependu, J. / Romer, W. / Varrot, A. / Imberty, A.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Fucose-Binding Lectin from Opportunistic Pathogen Burkholderia Ambifaria Binds to Both Plant and Human Oligosaccharidic Epitopes.
Authors: Audfray, A. / Claudinon, J. / Abounit, S. / Ruvoen-Clouet, N. / Larson, G. / Smith, D.F. / Wimmerova, M. / Le Pendu, J. / Romer, W. / Varrot, A. / Imberty, A.
History
DepositionJul 28, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2011Group: Other
Revision 1.2Feb 15, 2012Group: Other
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / 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 / _atom_site.label_entity_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BAMBL LECTIN
B: BAMBL LECTIN
C: BAMBL LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2979
Polymers28,1613
Non-polymers3,1366
Water4,684260
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-41.3 kcal/mol
Surface area14230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.640, 47.570, 72.940
Angle α, β, γ (deg.)90.00, 103.19, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.87231, -0.05693, 0.48563), (-0.45523, -0.45702, 0.76413), (0.17844, -0.88763, -0.42458)-25.50875, 5.21028, 109.54422
2given(0.87341, -0.45396, 0.17627), (-0.06194, -0.46258, -0.88441), (0.48303, 0.76154, -0.43214)5.02234, 97.94873, 55.39693

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Components

#1: Protein BAMBL LECTIN


Mass: 9387.166 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BURKHOLDERIA AMBIFARIA (bacteria) / Strain: AMMD / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q0B4G1
#2: Polysaccharide
alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose / H type 1 antigen / beta anomer


Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 529.490 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: H type 1 antigen, beta anomer
DescriptorTypeProgram
LFucpa1-2DGalpb1-3DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][a1221m-1a_1-5]/1-2-3/a3-b1_b2-c1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 326.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-2DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][a1221m-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(2+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#4: Polysaccharide alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-alpha-D-galactopyranose


Type: oligosaccharide / Mass: 691.630 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-2DGalpb1-3DGlcpNAcb1-3DGalpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,4,3/[a2112h-1a_1-5][a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][a1221m-1a_1-5]/1-2-3-4/a3-b1_b3-c1_c2-d1WURCSPDB2Glycan 1.1.0
[][a-D-Galp]{[(3+1)][b-D-GlcpNAc]{[(3+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}}}}LINUCSPDB-CARE
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 1.99 Å3/Da / Density % sol: 38.28 % / Description: NONE
Crystal growpH: 6
Details: 3 M MALONATE PH 6.0. 10% ETHYLENE GLYCOL WAS ADDED AS CRYOPROTECTANT PRIOR FREEZING

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.1399
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 7, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1399 Å / Relative weight: 1
ReflectionResolution: 1.6→39.52 Å / Num. obs: 29207 / % possible obs: 95.3 % / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 7.1
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 2.5 / % possible all: 78.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZW0

3zw0


Resolution: 1.6→39.52 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.49 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.20235 1456 5 %RANDOM
Rwork0.16009 ---
obs0.16216 27618 94.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.239 Å2
Baniso -1Baniso -2Baniso -3
1-1.64 Å20 Å20.84 Å2
2---0.23 Å20 Å2
3----1.03 Å2
Refinement stepCycle: LAST / Resolution: 1.6→39.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1983 0 213 260 2456
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212306
X-RAY DIFFRACTIONr_bond_other_d0.0010.021417
X-RAY DIFFRACTIONr_angle_refined_deg1.6811.9913190
X-RAY DIFFRACTIONr_angle_other_deg1.22333379
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.835268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.25223.07791
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.63715269
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.5311512
X-RAY DIFFRACTIONr_chiral_restr0.1050.2388
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022470
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02489
X-RAY DIFFRACTIONr_nbd_refined0.1760.2297
X-RAY DIFFRACTIONr_nbd_other0.2010.21349
X-RAY DIFFRACTIONr_nbtor_refined0.1880.21090
X-RAY DIFFRACTIONr_nbtor_other0.0970.21187
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2205
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1440.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1880.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9041.51302
X-RAY DIFFRACTIONr_mcbond_other0.2651.5562
X-RAY DIFFRACTIONr_mcangle_it1.53222074
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.04731004
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8754.51115
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: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 82 -
Rwork0.265 1569 -
obs--72.57 %
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)
10.82770.3302-0.25642.28490.35541.86890.0285-0.09540.01540.1034-0.020.0222-0.0327-0.0109-0.00860.008-0.0024-0.00470.06980.00110.0195-15.912733.054963.6342
20.92350.1852-0.20381.85140.25812.81170.0157-0.04140.0665-0.045-0.01-0.0051-0.18780.015-0.00560.0304-0.00130.00610.00670.00350.0415-10.119746.124350.0825
30.8442-0.0975-0.42371.7372-0.21051.81650.0060.0027-0.0053-0.11640.0147-0.01310.0203-0.0201-0.02070.01260.0012-0.00910.0177-0.00530.0214-12.622727.074945.2715
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 87
2X-RAY DIFFRACTION2B1 - 87
3X-RAY DIFFRACTION3C1 - 87

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