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- PDB-5t50: LIGAND-FREE LECTIN FROM BAUHINIA FORFICATA -

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Basic information

Entry
Database: PDB / ID: 5t50
TitleLIGAND-FREE LECTIN FROM BAUHINIA FORFICATA
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 / MOLECULAR REPLACEMENT / 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 1.4Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lectin
B: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,94514
Polymers54,2882
Non-polymers65712
Water7,098394
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-43 kcal/mol
Surface area18530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.991, 58.004, 190.546
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

#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: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / 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: 2.49 Å3/Da / Density % sol: 50.58 % / Description: BLOCKS
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PROTEIN CONCENTRATION 5-8 MG/ML IN 0.05 M HEPES BUFFER (pH 7.5) AND 0.15 M NACL, PRECIPITANT: 12% (W/W) PEG8000, 8% (W/V) ETHYLENE GLYCOL, 0.1 M HEPES (pH 7.5), DROPLETS RATIO: 1:1
PH range: 7 - 8

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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: Sep 5, 2015
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: 90961 / % possible obs: 95.5 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.059 / Net I/av σ(I): 23.179 / Net I/σ(I): 8.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.43-1.452.50.4880.759163.9
1.45-1.4830.460.766174.1
1.48-1.513.30.4370.801183
1.51-1.543.60.4260.805191.1
1.54-1.574.10.3820.86197.5
1.57-1.614.60.3620.896199.4
1.61-1.654.90.3330.923199.8
1.65-1.75.10.2780.9511100
1.7-1.755.10.2280.964199.9
1.75-1.85.10.1870.9741100
1.8-1.875.10.1550.981100
1.87-1.945.10.1280.9851100
1.94-2.035.10.0970.9921100
2.03-2.145.10.0810.9931100
2.14-2.275.10.0690.9941100
2.27-2.455.10.0660.9941100
2.45-2.695.10.060.9951100
2.69-3.085.10.0420.9981100
3.08-3.885.10.030.9991100
3.88-504.80.0260.999199.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-3000data collection
HKL-3000data scaling
PDB_EXTRACT3.2data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HQL

1hql


Resolution: 1.43→30 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.691 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.054 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1605 4257 5 %RANDOM
Rwork0.1164 ---
obs0.1186 81670 89.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 108.81 Å2 / Biso mean: 17.109 Å2 / Biso min: 7.62 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å2-0 Å2-0 Å2
2---0.39 Å20 Å2
3---0.59 Å2
Refinement stepCycle: final / Resolution: 1.43→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3622 0 36 395 4053
Biso mean--27.03 30.31 -
Num. residues----458
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0193868
X-RAY DIFFRACTIONr_bond_other_d0.0010.023526
X-RAY DIFFRACTIONr_angle_refined_deg1.9861.9215276
X-RAY DIFFRACTIONr_angle_other_deg1.28138096
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2855468
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.17723.198197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.8915577
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5711530
X-RAY DIFFRACTIONr_chiral_restr0.1360.2580
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214435
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02995
X-RAY DIFFRACTIONr_mcbond_it2.2941.3241845
X-RAY DIFFRACTIONr_mcbond_other2.2251.321844
X-RAY DIFFRACTIONr_mcangle_it2.3911.9962307
X-RAY DIFFRACTIONr_rigid_bond_restr5.75737394
X-RAY DIFFRACTIONr_sphericity_free33.7885127
X-RAY DIFFRACTIONr_sphericity_bonded11.62757562
LS refinement shellResolution: 1.428→1.465 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 136 -
Rwork0.252 2977 -
all-3113 -
obs--44.73 %

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