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- PDB-8yj9: Crystallization Studies of Concanavalin A in-Complex with D-Arabinose -

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Basic information

Entry
Database: PDB / ID: 8yj9
TitleCrystallization Studies of Concanavalin A in-Complex with D-Arabinose
ComponentsConcanavalin-Br
KeywordsSUGAR BINDING PROTEIN / D-Arabinose / Plant Lectin
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
: / L-ribose / Concanavalin-Br
Similarity search - Component
Biological speciesCanavalia ensiformis (jack bean)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsRasheed, S. / Arif, R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystallization Studies of Concanavalin A in-Complex with D-Arabinose
Authors: Rasheed, S. / Arif, R.
History
DepositionMar 1, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 5, 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)26,3369
Polymers25,6221
Non-polymers7148
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.882, 86.627, 88.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-427-

HOH

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Components

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Protein / Sugars , 2 types, 2 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
#3: Sugar ChemComp-ROR / L-ribose


Type: L-saccharide / Mass: 150.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10O5 / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 5 types, 127 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CA / CALCIUM ION


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


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


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.28 Å3/Da / Density % sol: 46.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: Crystallization solution was comprised of sodium acetate (100 mM, pH=5), PEG6000 (5%), and Ammoniun Sulphate (2M) in hanging drop vapor diffusion setup.
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: Nov 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 2.2→21.9 Å / Num. obs: 12438 / % possible obs: 99.9 % / Redundancy: 5.5 % / CC1/2: 0.967 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.088 / Rrim(I) all: 0.21 / Net I/σ(I): 35.2
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 5.5 / Num. unique obs: 1064 / CC1/2: 0.737 / Rpim(I) all: 0.298 / Rrim(I) all: 0.585 / % 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: 2.2→21.9 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.912 / SU B: 5.49 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.268 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22135 647 5.2 %RANDOM
Rwork0.16889 ---
obs0.17176 11789 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.372 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å2-0 Å20 Å2
2---0.65 Å2-0 Å2
3----0.45 Å2
Refinement stepCycle: 1 / Resolution: 2.2→21.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1837 0 12 120 1969
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0121883
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161716
X-RAY DIFFRACTIONr_angle_refined_deg1.3291.642562
X-RAY DIFFRACTIONr_angle_other_deg0.4711.5733968
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0995236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.67256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.77610289
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0630.2298
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022159
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02413
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_it1.3421.411947
X-RAY DIFFRACTIONr_mcbond_other1.341.412947
X-RAY DIFFRACTIONr_mcangle_it2.2992.5311182
X-RAY DIFFRACTIONr_mcangle_other2.2992.5321183
X-RAY DIFFRACTIONr_scbond_it1.8071.651936
X-RAY DIFFRACTIONr_scbond_other1.7691.615929
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8582.8561369
X-RAY DIFFRACTIONr_long_range_B_refined5.17817.462096
X-RAY DIFFRACTIONr_long_range_B_other5.07417.22078
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 39 -
Rwork0.203 848 -
obs--99.89 %

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