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- PDB-5t55: LECTIN FROM BAUHINIA FORFICATA IN COMPLEX WITH GLOBOTETRAOSE -

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Basic information

Entry
Database: PDB / ID: 5t55
TitleLECTIN FROM BAUHINIA FORFICATA IN COMPLEX WITH GLOBOTETRAOSE
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, beta chain, Mn/Ca-binding site / Legume lectin domain / 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: 1.43 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: Advisory / Atomic model ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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_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 / _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.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_alt_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 / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _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)56,19519
Polymers54,2882
Non-polymers1,90717
Water7,296405
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint-21 kcal/mol
Surface area18630 Å2
Unit cell
Length a, b, c (Å)44.681, 88.233, 110.782
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsDIMER AS DETERMINED BY ANALYTICAL ULTRACENTRIFUGATION

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Components

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Protein , 1 types, 2 molecules AB

#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

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Sugars , 2 types, 2 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpNAcb1-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][a2112h-1b_1-5_2*NCC/3=O]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Galp]{[(3+1)][b-D-GalpNAc]{}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-alpha-D-galactopyranose-(1-4)-beta-D- ...2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 707.630 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpNAcb1-3DGalpa1-4DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,4,3/[a2122h-1b_1-5][a2112h-1b_1-5][a2112h-1a_1-5][a2112h-1b_1-5_2*NCC/3=O]/1-2-3-4/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(4+1)][a-D-Galp]{[(3+1)][b-D-GalpNAc]{}}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 420 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / 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: 2.01 Å3/Da / Density % sol: 38.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PROTEIN CONCENTRATION 5-8 MG/ML IN 0.05 M HEPES BUFFER (pH 7.5) AND 0.15 M NACL, PRECIPITANT: 28% (W/W) PEG6000, 0.5 M LITHIUM CHLORIDE, , 0.1 M TRIS (pH 8.5), 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 MX300-HS / Detector: CCD / Date: Feb 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.43→50 Å / Num. obs: 79081 / % possible obs: 96.5 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.019 / Rrim(I) all: 0.07 / Χ2: 0.959 / Net I/av σ(I): 36.789 / Net I/σ(I): 8.2 / Num. measured all: 1022165
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.43-1.454.70.47122870.8620.2130.520.78856.3
1.45-1.486.40.4433520.9120.1670.4730.8182.9
1.48-1.517.80.45136970.9360.1530.4780.82792.1
1.51-1.549.10.44439700.9440.1410.4670.84797.6
1.54-1.5710.40.42640350.9530.1290.4460.89299.8
1.57-1.6111.80.39640550.970.1160.4140.922100
1.61-1.65130.36740640.9780.1040.3820.937100
1.65-1.713.90.33840330.980.0940.3510.955100
1.7-1.7514.20.28840800.9860.0790.2990.986100
1.75-1.814.60.23240640.990.0630.2411.042100
1.8-1.8714.70.19340800.9920.0520.21.061100
1.87-1.9414.80.15640700.9940.0420.1621.082100
1.94-2.0314.80.12140710.9960.0320.1251.138100
2.03-2.1414.80.09941070.9970.0260.1031.1100
2.14-2.2714.80.08140860.9980.0220.0841.01100
2.27-2.4514.80.07241140.9980.0190.0751.005100
2.45-2.6914.80.06941280.9980.0180.0711.103100
2.69-3.0814.80.05141730.9990.0140.0520.919100
3.08-3.8814.70.03441980.9990.0090.0350.715100
3.88-50140.03144170.9990.0090.0320.65799.8

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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: 1.43→39.861 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.638 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.055 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1466 3713 4.9 %RANDOM
Rwork0.1047 ---
obs0.1067 71808 93.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 140.15 Å2 / Biso mean: 17.14 Å2 / Biso min: 7.19 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å2-0 Å2-0 Å2
2---1.12 Å20 Å2
3---1 Å2
Refinement stepCycle: final / Resolution: 1.43→39.861 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3622 0 126 406 4154
Biso mean--27.58 33.65 -
Num. residues----458
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.023902
X-RAY DIFFRACTIONr_bond_other_d0.0030.023533
X-RAY DIFFRACTIONr_angle_refined_deg1.9861.9455304
X-RAY DIFFRACTIONr_angle_other_deg2.57738122
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3055460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.81523.368190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.45215563
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.11526
X-RAY DIFFRACTIONr_chiral_restr0.1420.2594
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214378
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02974
X-RAY DIFFRACTIONr_mcbond_it2.0591.3131834
X-RAY DIFFRACTIONr_mcbond_other1.7371.311833
X-RAY DIFFRACTIONr_mcangle_it2.1781.9772290
X-RAY DIFFRACTIONr_rigid_bond_restr5.33437435
X-RAY DIFFRACTIONr_sphericity_free58.6265128
X-RAY DIFFRACTIONr_sphericity_bonded13.90157618
LS refinement shellResolution: 1.435→1.472 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.185 163 -
Rwork0.108 3237 -
all-3400 -
obs--57.55 %

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