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- PDB-3zw0: Structure of BambL lectin from Burkholderia ambifaria -

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Basic information

Entry
Database: PDB / ID: 3zw0
TitleStructure of BambL lectin from Burkholderia ambifaria
Components(BAMBL LECTIN) x 2
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 / alpha-L-fucopyranose / 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 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2012Group: Other
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 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)28,3424
Polymers28,1773
Non-polymers1641
Water7,188399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-16.8 kcal/mol
Surface area11420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.110, 47.250, 98.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.2951, -0.9092, 0.2938), (0.08808, 0.2803, 0.9559), (-0.9514, 0.3079, -0.002639)-6.53, 15.05, -23.14
2given(-0.2979, 0.1261, -0.9462), (-0.9006, 0.2916, 0.3224), (0.3166, 0.9482, 0.0267)-25.05, -2.763, -12.01

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Components

#1: Protein BAMBL LECTIN


Mass: 9387.166 Da / Num. of mol.: 2
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: Protein BAMBL LECTIN


Mass: 9403.166 Da / Num. of mol.: 1
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
#3: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose / Fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 399 / 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: 1.78 Å3/Da / Density % sol: 31.11 % / Description: NONE
Crystal growpH: 7.5 / Details: pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9334
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 16, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.6→33.24 Å / Num. obs: 26647 / % possible obs: 93.7 % / Observed criterion σ(I): 3 / Redundancy: 3.7 % / Biso Wilson estimate: 10.2 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 26.6
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.06 / Mean I/σ(I) obs: 13.4 / % possible all: 70.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BT9

2bt9


Resolution: 1.6→49.16 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.935 / SU B: 1.537 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.18842 1334 5 %RANDOM
Rwork0.14344 ---
obs0.14569 25224 93.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.177 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å20 Å2
2---0.17 Å20 Å2
3---0.61 Å2
Refinement stepCycle: LAST / Resolution: 1.6→49.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1984 0 11 399 2394
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212112
X-RAY DIFFRACTIONr_bond_other_d0.0010.021322
X-RAY DIFFRACTIONr_angle_refined_deg1.5371.882902
X-RAY DIFFRACTIONr_angle_other_deg0.84333180
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8685272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.78822.93592
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.60115273
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6021513
X-RAY DIFFRACTIONr_chiral_restr0.0960.2305
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022483
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02492
X-RAY DIFFRACTIONr_nbd_refined0.1550.2297
X-RAY DIFFRACTIONr_nbd_other0.230.21302
X-RAY DIFFRACTIONr_nbtor_refined0.1930.2948
X-RAY DIFFRACTIONr_nbtor_other0.1190.21051
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2273
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1690.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.242
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.921.51314
X-RAY DIFFRACTIONr_mcbond_other0.2761.5566
X-RAY DIFFRACTIONr_mcangle_it1.5422097
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1783798
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0654.5805
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
Rfree0.227 65 -
Rwork0.15 1293 -
obs--65.6 %

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