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- PDB-4l8q: Crystal structure of Canavalia grandiflora seed lectin complexed ... -

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Basic information

Entry
Database: PDB / ID: 4l8q
TitleCrystal structure of Canavalia grandiflora seed lectin complexed with X-Man.
ComponentsCanavalia grandiflora seed lectin
Keywordssugar binding protein / plant protein / Jelly roll domain / Lectin / Carbohydrate/Sugar Binding / Protein bodies
Function / homology
Function and homology information


mannose binding / 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, 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
: / : / Chem-XMM / Lectin ConGF
Similarity search - Component
Biological speciesCanavalia grandiflora (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsBarroso-Neto, I.L. / Rocha, B.A.M. / Simoes, R.C. / Bezerra, M.J.B. / Pereira-Junior, F.N. / Osterne, V.J.S. / Nascimento, K.S. / Nagano, C.S. / Delatorre, P. / Sampaio, A.H. / Cavada, B.S.
CitationJournal: Arch.Biochem.Biophys. / Year: 2014
Title: Vasorelaxant activity of Canavalia grandiflora seed lectin: A structural analysis.
Authors: Barroso-Neto, I.L. / Simoes, R.C. / Rocha, B.A. / Bezerra, M.J. / Pereira-Junior, F.N. / Silva Osterne, V.J. / Nascimento, K.S. / Nagano, C.S. / Delatorre, P. / Pereira, M.G. / Freitas ...Authors: Barroso-Neto, I.L. / Simoes, R.C. / Rocha, B.A. / Bezerra, M.J. / Pereira-Junior, F.N. / Silva Osterne, V.J. / Nascimento, K.S. / Nagano, C.S. / Delatorre, P. / Pereira, M.G. / Freitas Pires, A. / Sampaio, A.H. / Assreuy, A.M. / Cavada, B.S.
History
DepositionJun 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Jul 29, 2020Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Canavalia grandiflora seed lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,73010
Polymers25,6291
Non-polymers1,1019
Water1,58588
1
A: Canavalia grandiflora seed lectin
hetero molecules

A: Canavalia grandiflora seed lectin
hetero molecules

A: Canavalia grandiflora seed lectin
hetero molecules

A: Canavalia grandiflora seed lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,92140
Polymers102,5174
Non-polymers4,40336
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area15430 Å2
ΔGint-242 kcal/mol
Surface area31010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.422, 65.152, 106.708
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Canavalia grandiflora seed lectin


Mass: 25629.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canavalia grandiflora (plant) / References: UniProt: A0A067XG71*PLUS
#4: Sugar ChemComp-XMM / 5-bromo-4-chloro-1H-indol-3-yl alpha-D-mannopyranoside / (2R,3S,4S,5S,6R)-2-(5-BROMO-4-CHLORO-1H-INDOL-3-YLOXY)-TETRAHYDRO-6-(HYDROXYMETHYL)-2H-PYRAN-3,4,5-TRIOL / (5-BROMO-4-CHLORO-3-INDOLYL)-Alpha-D-MANNOSE / 5-bromo-4-chloro-1H-indol-3-yl alpha-D-mannoside / 5-bromo-4-chloro-1H-indol-3-yl D-mannoside / 5-bromo-4-chloro-1H-indol-3-yl mannoside


Type: D-saccharide / Mass: 408.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H15BrClNO6

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Non-polymers , 6 types, 96 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: 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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.18 Å3/Da / Density % sol: 43.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.05 M cadmium sulfate hydrate, 0.1 M HEPES buffer, and 1.0 M sodium acetate trihydrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.47 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 27, 2008
RadiationMonochromator: Curved crystal of silicon (111), asymmetrical cut. Asymmetry angle 7.25 , condensed mode. Range of photon energies of X-ray: 6 keV-12 keV (2 1 ). Dimensions: 250 mm x 50 mm (at the base) x 1 mm.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.47 Å / Relative weight: 1
ReflectionResolution: 2.3→10.29 Å / Num. all: 71496 / Num. obs: 10110 / % possible obs: 99.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 34.658 Å2 / Rmerge(I) obs: 0.138 / Net I/σ(I): 10
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.3-2.360.3165.165346746100
2.36-2.420.2915.555144724100
2.42-2.490.2695.974864680100
2.49-2.570.2276.84948687100
2.57-2.660.2067.434723657100
2.66-2.750.1838.314653646100
2.75-2.850.1738.454392615100
2.85-2.970.1599.69430859999.8
2.97-3.10.14510.834077564100
3.1-3.250.13712.184004557100
3.25-3.430.11912.813706516100
3.43-3.640.12213.483603504100
3.64-3.890.12313.83355475100
3.89-4.20.11614.17306643499.8
4.2-4.60.12114.59282740699.3
4.6-5.140.11814.41252136499.2
5.14-5.940.1214.14227133399.4
5.94-7.270.12514.33188528299.6
7.27-10.290.12513.82133722297.4
10.290.13612.54669970.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 32.27 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.3 Å19.17 Å
Translation2.3 Å19.17 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
MAR345data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2OVU

2ovu


Resolution: 2.3→10.29 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.893 / WRfactor Rfree: 0.2782 / WRfactor Rwork: 0.2413 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8025 / SU R Cruickshank DPI: 0.1119 / SU Rfree: 0.0592 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2668 506 5 %RANDOM
Rwork0.2258 ---
obs0.228 10109 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 94.19 Å2 / Biso mean: 34.4489 Å2 / Biso min: 11.02 Å2
Baniso -1Baniso -2Baniso -3
1-36.1 Å20 Å20 Å2
2---22.66 Å2-0 Å2
3----13.44 Å2
Refinement stepCycle: LAST / Resolution: 2.3→10.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1782 0 50 88 1920
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.021865
X-RAY DIFFRACTIONr_angle_refined_deg2.1211.972542
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1685231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.47225.12878
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.90415284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.974156
X-RAY DIFFRACTIONr_chiral_restr0.1260.2294
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211395
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 37 -
Rwork0.258 696 -
all-733 -
obs--99.86 %

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