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- PDB-8yya: Crystal Structure of Concanavalin A Complexed with 5-Fluorouracil -

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Basic information

Entry
Database: PDB / ID: 8yya
TitleCrystal Structure of Concanavalin A Complexed with 5-Fluorouracil
ComponentsConcanavalin-Br
KeywordsSUGAR BINDING PROTEIN / Plant Lectin / Canavalia ensiformis / jack beans
Function / homology
Function and homology information


D-mannose binding / toxin activity / metal ion binding
Similarity search - Function
Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / : / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
: / 5-FLUOROURACIL / Concanavalin-Br
Similarity search - Component
Biological speciesCanavalia ensiformis (jack bean)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.96 Å
AuthorsRasheed, S. / Arif, R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal Structure of Concanavalin A Complexed with 5-Fluorouracil
Authors: Rasheed, S. / Arif, R.
History
DepositionApr 3, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Concanavalin-Br
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9445
Polymers25,6221
Non-polymers3214
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-12 kcal/mol
Surface area10430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.781, 86.546, 88.637
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Concanavalin-Br / Con Br


Mass: 25622.385 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canavalia ensiformis (jack bean) / References: UniProt: P55915

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Non-polymers , 5 types, 17 molecules

#2: Chemical ChemComp-URF / 5-FLUOROURACIL


Mass: 130.077 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H3FN2O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.31 Å3/Da / Density % sol: 46.8 %
Crystal growTemperature: 293.5 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0. 1M Sodium Accetate buffer pH 5.0 , 5% PEG 6000, 2 M Ammonium Sulphate.
PH range: 4.5-5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.5406 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Dec 19, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 2.94→20.74 Å / Num. obs: 5189 / % possible obs: 99.7 % / Redundancy: 1.8 % / CC1/2: 0.91 / Rmerge(I) obs: 0.175 / Net I/σ(I): 11.8
Reflection shellResolution: 2.94→3.14 Å / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 5.3 / Num. unique obs: 829 / CC1/2: 0.722 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
PROTEUM PLUSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.96→20.74 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.797 / SU B: 21.426 / SU ML: 0.383 / Cross valid method: THROUGHOUT / ESU R Free: 0.507 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27389 283 5.5 %RANDOM
Rwork0.19477 ---
obs0.19918 4905 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 5.397 Å2
Baniso -1Baniso -2Baniso -3
1-3.04 Å20 Å2-0 Å2
2---1.99 Å2-0 Å2
3----1.05 Å2
Refinement stepCycle: 1 / Resolution: 2.96→20.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1809 0 16 13 1838
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0121868
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161695
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.6362548
X-RAY DIFFRACTIONr_angle_other_deg0.4841.5723916
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.3395236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.78356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.1410289
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0620.2292
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022165
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02415
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7760.548947
X-RAY DIFFRACTIONr_mcbond_other0.7760.548947
X-RAY DIFFRACTIONr_mcangle_it1.4570.9841182
X-RAY DIFFRACTIONr_mcangle_other1.4560.9841183
X-RAY DIFFRACTIONr_scbond_it0.5810.608921
X-RAY DIFFRACTIONr_scbond_other0.5540.578914
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.0891.0441355
X-RAY DIFFRACTIONr_long_range_B_refined2.6775.82054
X-RAY DIFFRACTIONr_long_range_B_other2.6765.812055
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.96→3.035 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 24 -
Rwork0.274 344 -
obs--100 %

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