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- PDB-5t54: LECTIN FROM BAUHINIA FORFICATA IN COMPLEX WITH BLOOD GROUP A ANTIGEN -

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Basic information

Entry
Database: PDB / ID: 5t54
TitleLECTIN FROM BAUHINIA FORFICATA IN COMPLEX WITH BLOOD GROUP A ANTIGEN
ComponentsLectin
KeywordsSUGAR BINDING PROTEIN / LEGUME LECTIN / CONCANAVALIN A / GALNAC-SPECIFIC / LIGAND-FREE
Function / homology
Function and homology information


carbohydrate binding / extracellular region / metal ion binding
Similarity search - Function
Legume lectin / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / : / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesBauhinia forficata (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.65 Å
AuthorsLubkowski, J. / Wlodawer, A.
CitationJournal: FEBS J. / Year: 2017
Title: Structural analysis and unique molecular recognition properties of a Bauhinia forficata lectin that inhibits cancer cell growth.
Authors: Lubkowski, J. / Durbin, S.V. / Silva, M.C. / Farnsworth, D. / Gildersleeve, J.C. / Oliva, M.L. / Wlodawer, A.
History
DepositionAug 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2017Group: Database references
Revision 1.2Feb 15, 2017Group: Database references
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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_conn_angle / refine_hist / struct_asym / struct_conn / struct_conn_type / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _refine_hist.d_res_low / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _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.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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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)55,75512
Polymers54,2882
Non-polymers1,46810
Water6,720373
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-25 kcal/mol
Surface area18180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.829, 44.820, 65.771
Angle α, β, γ (deg.)90.000, 100.050, 90.000
Int Tables number4
Space group name H-MP1211
DetailsDIMER AS DETERMINED BY ANALYTICAL ULTRACENTRIFUGATION

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Components

#1: Protein Lectin / BfL


Mass: 27143.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bauhinia forficata (plant) / Production host: Escherichia coli (E. coli) / References: UniProt: P86993
#2: Polysaccharide alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]alpha-D-galactopyranose


Type: oligosaccharide / Mass: 529.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-2[DGalpNAca1-3]DGalpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2112h-1a_1-5][a1221m-1a_1-5][a2112h-1a_1-5_2*NCC/3=O]/1-2-3/a2-b1_a3-c1WURCSPDB2Glycan 1.1.0
[][a-D-Galp]{[(2+1)][a-L-Fucp]{}[(3+1)][a-D-GalpNAc]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / 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: 2.11 Å3/Da / Density % sol: 41.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: PROTEIN CONCENTRATION 5-8 MG/ML IN 0.05 M HEPES BUFFER (pH 7.5) AND 0.15 M NACL, PRECIPITANT: 25% (W/W) PEG1500, 0.1 M NACL, 0.1 M BIS-TRI PROPANE (pH 9.0), DROPLETS RATIO: 1:1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX340-HS / Detector: CCD / Date: Sep 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 52931 / % possible obs: 96.9 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.039 / Rrim(I) all: 0.075 / Χ2: 0.827 / Net I/av σ(I): 15.661 / Net I/σ(I): 8.4 / Num. measured all: 178921
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.65-1.682.20.30.885174.3
1.68-1.712.70.3110.88194.4
1.71-1.743.10.3020.909199.8
1.74-1.783.20.2650.9221100
1.78-1.823.30.2240.944199.7
1.82-1.863.40.2040.943199.7
1.86-1.93.40.1760.952199.4
1.9-1.963.40.1560.957199.3
1.96-2.013.50.1270.965199.1
2.01-2.083.50.1090.969198.9
2.08-2.153.50.1040.974198.8
2.15-2.243.50.0940.977198.3
2.24-2.343.50.0850.979198.2
2.34-2.463.50.0760.984198.2
2.46-2.623.60.0680.985198.2
2.62-2.823.60.0570.991197.6
2.82-3.113.60.0580.99197.4
3.11-3.553.60.050.994196.9
3.55-4.483.60.0420.995195.9
4.48-503.60.0360.997193.9

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000data scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.2data extraction
HKL-3000data reduction
PHASERphasing
RefinementResolution: 1.65→38.814 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.284 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1771 2601 5.1 %RANDOM
Rwork0.1496 ---
obs0.1511 48757 93.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 71.19 Å2 / Biso mean: 15.924 Å2 / Biso min: 6.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å2-0 Å2-0.09 Å2
2---0.66 Å2-0 Å2
3----0.24 Å2
Refinement stepCycle: final / Resolution: 1.65→38.814 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3622 0 92 373 4087
Biso mean--20.95 25.69 -
Num. residues----458
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0193844
X-RAY DIFFRACTIONr_bond_other_d0.0010.023443
X-RAY DIFFRACTIONr_angle_refined_deg2.0161.9425248
X-RAY DIFFRACTIONr_angle_other_deg1.44437907
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.425456
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.69823.511188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.73715544
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3231524
X-RAY DIFFRACTIONr_chiral_restr0.130.2592
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0214354
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02964
X-RAY DIFFRACTIONr_mcbond_it0.8750.7391830
X-RAY DIFFRACTIONr_mcbond_other0.8690.7371829
X-RAY DIFFRACTIONr_mcangle_it1.3871.1022284
LS refinement shellResolution: 1.651→1.694 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 124 -
Rwork0.23 2297 -
all-2421 -
obs--60.33 %
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)
10.4201-0.1437-0.1180.48430.11280.34530.012-0.0080.0165-0.0259-0.00420.0142-0.0175-0.0115-0.00790.00390.00070.00910.08810.0130.04541.86833.97720.849
21.49020.0681-0.01380.83820.00560.20660.01950.0092-0.1470.02460.0546-0.0522-0.01050.0047-0.07410.0020.00710.00270.07490.00490.071128.76919.7829.737
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 229
2X-RAY DIFFRACTION1A301 - 305
3X-RAY DIFFRACTION2B1 - 229
4X-RAY DIFFRACTION2B301 - 305

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