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- PDB-3zw1: Structure of Bambl lectine in complex with lewix x antigen -

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Basic information

Entry
Database: PDB / ID: 3zw1
TitleStructure of Bambl lectine in complex with lewix x antigen
Components(BAMBL LECTIN) x 2
KeywordsSUGAR BINDING PROTEIN / FUCOSE BINDING LECTIN
Function / homologyLipocalin - #190 / Fucose-specific lectin / Fungal fucose-specific lectin / Lipocalin / Beta Barrel / Mainly Beta / alpha-D-galactopyranose / Fucose-binding lectin protein / 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: Plos One / Year: 2013
Title: Deciphering the Glycan Preference of Bacterial Lectins by Glycan Array and Molecular Docking with Validation by Microcalorimetry and Crystallography.
Authors: Topin, J. / Arnaud, J. / Sarkar, A. / Audfray, A. / Gillon, E. / Perez, S. / Jamet, H. / Varrot, A. / Imberty, A. / Thomas, A.
History
DepositionJul 28, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / 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_special_symmetry / struct_asym / struct_conn / 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_alt_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 / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _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.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_comp_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
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0887
Polymers18,7902
Non-polymers2,2985
Water4,270237
1
A: BAMBL LECTIN
hetero molecules

A: BAMBL LECTIN
hetero molecules

A: BAMBL LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3869
Polymers28,2093
Non-polymers3,1776
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_545-y,z-1/2,-x+1/21
crystal symmetry operation7_555-z+1/2,-x,y+1/21
Buried area5260 Å2
ΔGint-37.3 kcal/mol
Surface area14990 Å2
MethodPISA
2
B: BAMBL LECTIN
hetero molecules

B: BAMBL LECTIN
hetero molecules

B: BAMBL LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,87912
Polymers28,1613
Non-polymers3,7179
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation5_555z,x,y1
Buried area5110 Å2
ΔGint-36.6 kcal/mol
Surface area15010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.440, 81.440, 81.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-2003-

HOH

21A-2004-

HOH

31A-2008-

HOH

41B-2002-

HOH

51B-2004-

HOH

61B-2027-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.94918, 0.24442, -0.19829), (-0.24967, -0.20113, 0.94721), (0.19163, 0.94858, 0.25194)
Vector: 10.78935, -35.84144, -7.33737)

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Components

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Protein , 2 types, 2 molecules AB

#1: 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) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYS / References: UniProt: B1Z019, UniProt: Q0B4G1*PLUS
#2: Protein BAMBL LECTIN


Mass: 9387.166 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BURKHOLDERIA AMBIFARIA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYS / References: UniProt: B1Z019, UniProt: Q0B4G1*PLUS

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Sugars , 3 types, 5 molecules

#3: Polysaccharide alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#4: Polysaccharide alpha-L-fucopyranose-(1-3)-[beta-D-galactopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose- ...alpha-L-fucopyranose-(1-3)-[beta-D-galactopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 691.630 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[DGalpb1-4]DGlcpNAcb1-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2112h-1b_1-5][a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-3-1/a3-b1_b3-c1_b4-d1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-Galp]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-GLA / alpha-D-galactopyranose / alpha-D-galactose / D-galactose / galactose / ALPHA D-GALACTOSE


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-galactopyranoseCOMMON NAMEGMML 1.0
a-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 1 types, 237 molecules

#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.3 Å3/Da / Density % sol: 46.54 % / Description: NONE
Crystal growpH: 5
Details: 28 % PEG 6000, 100MM SODIUM ACETATE PH 5.0, 200MM TRISODIUM CITRATE. 10% ETHYLENE GLYCOL WAD ADDED AS CRYOPROTECTANT PRIOR TO 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→40.72 Å / Num. obs: 23162 / % possible obs: 96.2 % / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 26.6
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 7.9 / % possible all: 82.4

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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→40.72 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.263 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. DISORDERED SIDE CHAINS WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.18904 1180 5.1 %RANDOM
Rwork0.15331 ---
obs0.1551 21930 96.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.28 Å2
Refinement stepCycle: LAST / Resolution: 1.6→40.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1323 0 156 237 1716
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211556
X-RAY DIFFRACTIONr_bond_other_d0.0010.02951
X-RAY DIFFRACTIONr_angle_refined_deg1.7091.9952155
X-RAY DIFFRACTIONr_angle_other_deg0.89432275
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8925181
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.42623.22662
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.6215178
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.653158
X-RAY DIFFRACTIONr_chiral_restr0.1040.2262
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021671
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02329
X-RAY DIFFRACTIONr_nbd_refined0.2410.2186
X-RAY DIFFRACTIONr_nbd_other0.1980.2891
X-RAY DIFFRACTIONr_nbtor_refined0.1830.2723
X-RAY DIFFRACTIONr_nbtor_other0.0880.2782
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2148
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0280.21
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1770.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.230
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0811.5877
X-RAY DIFFRACTIONr_mcbond_other0.2891.5377
X-RAY DIFFRACTIONr_mcangle_it1.88221398
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3053679
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3714.5756
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: 1.601→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 77 -
Rwork0.203 1308 -
obs--79.19 %

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