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- PDB-5t5l: LECTIN FROM BAUHINIA FORFICATA IN COMPLEX WITH TN-PEPTIDE -

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Basic information

Entry
Database: PDB / ID: 5t5l
TitleLECTIN FROM BAUHINIA FORFICATA IN COMPLEX WITH TN-PEPTIDE
Components
  • Lectin
  • TN ANTIGEN ACE-SER-SER-VAL-GLY
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
2-acetamido-2-deoxy-alpha-D-galactopyranose / Lectin
Similarity search - Component
Biological speciesBauhinia forficata (plant)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.17 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 31, 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_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / refine_hist / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_ptnr1_label_alt_id / _struct_conn.pdbx_role / _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.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lectin
B: Lectin
a: TN ANTIGEN ACE-SER-SER-VAL-GLY
b: TN ANTIGEN ACE-SER-SER-VAL-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,38822
Polymers55,0374
Non-polymers1,35118
Water8,719484
1
A: Lectin
a: TN ANTIGEN ACE-SER-SER-VAL-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,13010
Polymers27,5182
Non-polymers6128
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lectin
b: TN ANTIGEN ACE-SER-SER-VAL-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,25812
Polymers27,5182
Non-polymers73910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.865, 88.502, 110.783
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 / Protein/peptide / Sugars , 3 types, 6 molecules ABab

#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: Protein/peptide TN ANTIGEN ACE-SER-SER-VAL-GLY


Mass: 374.391 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#7: Sugar ChemComp-A2G / 2-acetamido-2-deoxy-alpha-D-galactopyranose


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGalpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-galactopyranosamineCOMMON NAMEGMML 1.0
a-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 500 molecules

#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.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 484 / 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 Å3/Da / Density % sol: 38.51 %
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-TRIS 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 MX300-HS / Detector: CCD / Date: Nov 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.17→50 Å / Num. obs: 147131 / % possible obs: 98.5 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.032 / Rrim(I) all: 0.085 / Χ2: 0.919 / Net I/av σ(I): 17.386 / Net I/σ(I): 11.7 / Num. measured all: 1008306
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.17-1.194.20.44657010.810.2370.5070.79977.1
1.19-1.215.90.4373750.8730.1920.4720.82899.8
1.21-1.246.60.38973640.910.1640.4230.871100
1.24-1.266.80.3573930.9290.1450.3790.909100
1.26-1.296.90.30274170.9440.1240.3270.92100
1.29-1.326.90.26273790.9580.1070.2830.939100
1.32-1.356.90.23473860.9640.0960.2540.948100
1.35-1.3970.20574370.970.0830.2210.967100
1.39-1.4370.17774060.9730.0720.1910.977100
1.43-1.477.10.15674220.9770.0630.1680.977100
1.47-1.537.10.13674300.9830.0550.1470.96100
1.53-1.597.10.1274160.9850.0480.130.963100
1.59-1.667.20.10574910.9890.0420.1140.905100
1.66-1.757.20.09774380.990.0390.1040.892100
1.75-1.867.20.09474730.9890.0370.1020.952100
1.86-27.20.09474870.9910.0370.1011.048100
2-2.27.30.08775200.9920.0340.0930.981100
2.2-2.527.30.0875710.9930.0320.0860.933100
2.52-3.187.20.07376430.9940.0290.0780.834100
3.18-506.30.06373820.9930.0270.0690.64393

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000data scaling
REFMAC5.8.0107refinement
PDB_EXTRACT3.2data extraction
HKL-3000data reduction
PHASERphasing
RefinementResolution: 1.17→30.3 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.98 / SU B: 0.678 / SU ML: 0.014 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.027 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1301 4270 3 %RANDOM
Rwork0.1073 ---
obs0.108 139485 97.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 216.25 Å2 / Biso mean: 19.997 Å2 / Biso min: 10.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å2-0 Å2
2---0.53 Å20 Å2
3---0.03 Å2
Refinement stepCycle: final / Resolution: 1.17→30.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3670 0 79 486 4235
Biso mean--23.96 35.87 -
Num. residues----467
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193945
X-RAY DIFFRACTIONr_bond_other_d0.0010.023574
X-RAY DIFFRACTIONr_angle_refined_deg1.9851.9355365
X-RAY DIFFRACTIONr_angle_other_deg3.12738221
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.455467
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.49723.25200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.36615581
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1851528
X-RAY DIFFRACTIONr_chiral_restr0.1610.2589
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0214501
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02997
X-RAY DIFFRACTIONr_mcbond_it2.4981.5791876
X-RAY DIFFRACTIONr_mcbond_other2.4221.5771875
X-RAY DIFFRACTIONr_mcangle_it2.9882.372341
X-RAY DIFFRACTIONr_rigid_bond_restr6.02237519
X-RAY DIFFRACTIONr_sphericity_free43.6945128
X-RAY DIFFRACTIONr_sphericity_bonded14.70957783
LS refinement shellResolution: 1.173→1.204 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 208 -
Rwork0.195 7508 -
all-7716 -
obs--71.37 %

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