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- PDB-4aoc: crystal structure of BC2L-A Lectin from Burkolderia cenocepacia i... -

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Basic information

Entry
Database: PDB / ID: 4aoc
Titlecrystal structure of BC2L-A Lectin from Burkolderia cenocepacia in complex with methyl-heptoside
ComponentsBC2L-A LECTIN
KeywordsHYDROLASE
Function / homology
Function and homology information


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
methyl L-glycero-alpha-D-manno-heptopyranoside / PA-IIL domain-containing protein / PA-IIL domain-containing protein
Similarity search - Component
Biological speciesBURKHOLDERIA CENOCEPACIA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMarchetti, R. / Malinovska, L. / Lameignere, E. / deCastro, C. / Cioci, G. / Kosma, P. / Wimmerova, M. / Molinaro, A. / Imberty, A. / Silipo, A.
CitationJournal: Glycobiology / Year: 2012
Title: Burkholderia Cenocepacia Lectin a Binding to Heptoses from the Bacterial Lipopolysaccharide.
Authors: Marchetti, R. / Malinovska, L. / Lameignere, E. / Adamova, L. / De Castro, C. / Cioci, G. / Stanetty, C. / Kosma, P. / Molinaro, A. / Wimmerova, M. / Imberty, A. / Silipo, A.
History
DepositionMar 26, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references
Revision 1.2Nov 19, 2014Group: Data collection
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Other
Category: chem_comp / pdbx_database_status ...chem_comp / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _pdbx_database_status.status_code_sf ..._chem_comp.mon_nstd_flag / _pdbx_database_status.status_code_sf / _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_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _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 / _struct_conn.pdbx_dist_value / _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.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BC2L-A LECTIN
B: BC2L-A LECTIN
C: BC2L-A LECTIN
D: BC2L-A LECTIN
E: BC2L-A LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,13031
Polymers69,5515
Non-polymers2,57926
Water2,018112
1
A: BC2L-A LECTIN
B: BC2L-A LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,71711
Polymers27,8202
Non-polymers8979
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-73.4 kcal/mol
Surface area10760 Å2
MethodPISA
2
C: BC2L-A LECTIN
E: BC2L-A LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,81312
Polymers27,8202
Non-polymers99310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-103.9 kcal/mol
Surface area10880 Å2
MethodPISA
3
D: BC2L-A LECTIN
hetero molecules

D: BC2L-A LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,19816
Polymers27,8202
Non-polymers1,37714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3700 Å2
ΔGint-83.1 kcal/mol
Surface area10520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.000, 185.140, 186.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11D-1133-

SO4

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Components

#1: Protein
BC2L-A LECTIN


Mass: 13910.230 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BURKHOLDERIA CENOCEPACIA (bacteria) / Strain: AU 1054 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q1BKJ8, UniProt: A0A0H2Y045*PLUS
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#3: Sugar
ChemComp-A1Q / methyl L-glycero-alpha-D-manno-heptopyranoside / ALPHA-METHYL HEPTOPYRANOSE / methyl L-glycero-alpha-D-manno-heptoside / methyl L-glycero-D-manno-heptoside / methyl L-glycero-manno-heptoside


Type: D-saccharide / Mass: 224.208 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C8H16O7
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.95 Å3/Da / Density % sol: 58.3 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Details: KB MIRROR
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.7→48.27 Å / Num. obs: 24256 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 10.2
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.9 / % possible all: 81.7

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WR9

2wr9


Resolution: 2.7→93.11 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.88 / SU B: 10.79 / SU ML: 0.218 / Cross valid method: THROUGHOUT / ESU R: 0.605 / ESU R Free: 0.319 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2532 1236 5.1 %RANDOM
Rwork0.19228 ---
obs0.19545 23002 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.226 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å20 Å20 Å2
2--0 Å20 Å2
3----0.81 Å2
Refinement stepCycle: LAST / Resolution: 2.7→93.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4543 0 140 112 4795
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.024813
X-RAY DIFFRACTIONr_bond_other_d0.0010.023215
X-RAY DIFFRACTIONr_angle_refined_deg1.5691.9656553
X-RAY DIFFRACTIONr_angle_other_deg0.90137843
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8455601
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.50224.612232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.08615709
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1441526
X-RAY DIFFRACTIONr_chiral_restr0.0870.2718
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215412
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02966
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.452 78 -
Rwork0.307 1514 -
obs--95.85 %

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