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- PDB-5t5j: LECTIN FROM BAUHINIA FORFICATA IN COMPLEX WITH TN-PEPTIDE -

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Basic information

Entry
Database: PDB / ID: 5t5j
TitleLECTIN FROM BAUHINIA FORFICATA IN COMPLEX WITH TN-PEPTIDE
Components
  • Lectin
  • TN ANTIGEN ACA-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: 1.35 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_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
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
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.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_label_atom_id

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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 ACA-SER-SER-VAL-GLY
b: TN ANTIGEN ACA-SER-SER-VAL-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,24817
Polymers55,2114
Non-polymers1,03713
Water8,773487
1
A: Lectin
a: TN ANTIGEN ACA-SER-SER-VAL-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,21710
Polymers27,6052
Non-polymers6128
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lectin
b: TN ANTIGEN ACA-SER-SER-VAL-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0317
Polymers27,6052
Non-polymers4265
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.378, 46.159, 92.107
Angle α, β, γ (deg.)90.000, 92.560, 90.000
Int Tables number4
Space group name H-MP1211
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 ACA-SER-SER-VAL-GLY


Mass: 461.511 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#5: Sugar ChemComp-A2G / 2-acetamido-2-deoxy-alpha-D-galactopyranose / N-acetyl-alpha-D-galactosamine / 2-acetamido-2-deoxy-alpha-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE


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 , 3 types, 498 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.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 487 / 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: 2.1 Å3/Da / Density % sol: 41.38 %
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).PROTEIN CONCENTRATION 5-8 ...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).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 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: Mar 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→40 Å / Num. obs: 100009 / % possible obs: 99.9 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.027 / Rrim(I) all: 0.079 / Χ2: 1.054 / Net I/av σ(I): 27.626 / Net I/σ(I): 9 / Num. measured all: 793282
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.35-1.375.70.72349510.7610.3220.7940.6999.6
1.37-1.46.80.69950000.8380.2850.7560.686100
1.4-1.437.40.63149710.8750.2480.6780.695100
1.43-1.457.70.54949360.9080.210.5890.744100
1.45-1.497.90.47250050.9230.1770.5050.772100
1.49-1.5280.40149320.9430.1490.4290.788100
1.52-1.568.10.32750160.9550.1210.350.823100
1.56-1.68.10.27149510.9660.10.290.875100
1.6-1.658.20.22950240.9710.0850.2450.93100
1.65-1.78.20.19549720.9770.0720.2080.958100
1.7-1.768.20.16849750.9810.0620.1791.115100
1.76-1.838.20.1450030.9850.0520.1491.267100
1.83-1.928.20.12149890.9870.0450.1291.401100
1.92-2.028.30.10150020.9910.0370.1081.598100
2.02-2.148.30.09249990.9910.0340.0981.707100
2.14-2.318.30.08750090.9920.0320.0921.908100
2.31-2.548.30.07850280.9940.0280.0831.14100
2.54-2.918.30.06550350.9940.0240.0690.968100
2.91-3.668.30.05450680.9960.020.0580.853100
3.66-407.90.04851430.9960.0180.0520.8499.1

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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: 1.35→32.586 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.978 / SU B: 1.274 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.041 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1407 2927 3 %RANDOM
Rwork0.1053 ---
obs0.1064 93776 96.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 182.21 Å2 / Biso mean: 18.22 Å2 / Biso min: 7.21 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å2-0 Å2-0.05 Å2
2---0.62 Å20 Å2
3---0.91 Å2
Refinement stepCycle: final / Resolution: 1.35→32.586 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3671 0 60 487 4218
Biso mean--23.22 35.7 -
Num. residues----466
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0193899
X-RAY DIFFRACTIONr_bond_other_d0.0020.023561
X-RAY DIFFRACTIONr_angle_refined_deg2.0621.9325300
X-RAY DIFFRACTIONr_angle_other_deg2.13538184
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0895461
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.11723.333192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.34915577
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.311527
X-RAY DIFFRACTIONr_chiral_restr0.1530.2587
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0214412
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02985
X-RAY DIFFRACTIONr_mcbond_it1.9511.3981856
X-RAY DIFFRACTIONr_mcbond_other1.9371.3961855
X-RAY DIFFRACTIONr_mcangle_it2.1582.1032313
X-RAY DIFFRACTIONr_rigid_bond_restr5.82837459
X-RAY DIFFRACTIONr_sphericity_free37.4175174
X-RAY DIFFRACTIONr_sphericity_bonded14.41357681
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.196 142 -
Rwork0.137 4617 -
all-4759 -
obs--64.4 %

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