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- PDB-5f5q: Crystal structure of Canavalia virosa lectin in complex with alph... -

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Basic information

Entry
Database: PDB / ID: 5f5q
TitleCrystal structure of Canavalia virosa lectin in complex with alpha-methyl-mannoside
ComponentsConcanavalin-A
KeywordsSUGAR BINDING PROTEIN / METAL BINDING PROTEIN
Function / homology
Function and homology information


glucose binding / mannose binding / vasodilation / manganese ion binding / calcium ion 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
methyl alpha-D-mannopyranoside / : / Concanavalin V / Concanavalin-A
Similarity search - Component
Biological speciesCanavalia cathartica (xiao dao dou)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsOsterne, V.J.S. / Silva-Filho, J.C. / Pinto-Junior, V.R. / Santiago, M.Q. / Lossio, C.F. / Delatorre, P. / Nascimento, K.S. / Cavada, B.S.
CitationJournal: Int.J.Biol.Macromol. / Year: 2016
Title: Structural characterization of a lectin from Canavalia virosa seeds with inflammatory and cytotoxic activities.
Authors: Osterne, V.J. / Silva-Filho, J.C. / Santiago, M.Q. / Pinto-Junior, V.R. / Almeida, A.C. / Barreto, A.A. / Wolin, I.A. / Nascimento, A.P. / Amorim, R.M. / Rocha, B.A. / Delatorre, P. / ...Authors: Osterne, V.J. / Silva-Filho, J.C. / Santiago, M.Q. / Pinto-Junior, V.R. / Almeida, A.C. / Barreto, A.A. / Wolin, I.A. / Nascimento, A.P. / Amorim, R.M. / Rocha, B.A. / Delatorre, P. / Nagano, C.S. / Leal, R.B. / Assreuy, A.M. / Nascimento, K.S. / Cavada, B.S.
History
DepositionDec 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Database references
Revision 1.2Aug 9, 2017Group: Database references / Derived calculations / Category: citation / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / 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 / _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 / _struct_conn.pdbx_dist_value / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 27, 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: Concanavalin-A
B: Concanavalin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5878
Polymers51,0082
Non-polymers5786
Water1,76598
1
A: Concanavalin-A
B: Concanavalin-A
hetero molecules

A: Concanavalin-A
B: Concanavalin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,17416
Polymers102,0174
Non-polymers1,15712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area11220 Å2
ΔGint-105 kcal/mol
Surface area30990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.250, 81.740, 86.930
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein Concanavalin-A / Con A


Mass: 25504.232 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Canavalia cathartica (xiao dao dou) / Organ: Seed / References: UniProt: P81461, UniProt: C0HJY1*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Sugar ChemComp-MMA / methyl alpha-D-mannopyranoside / O1-METHYL-MANNOSE / methyl alpha-D-mannoside / methyl D-mannoside / methyl mannoside / Methylglucoside


Type: D-saccharide / Mass: 194.182 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C7H14O6
IdentifierTypeProgram
DManp[1Me]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-a-D-mannopyranoseCOMMON NAMEGMML 1.0
o1-methyl-mannoseIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 300 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: Tris-HCl, Ammonium sulphate, Glycerol / PH range: 8.2-8.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.47 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.47 Å / Relative weight: 1
ReflectionResolution: 2.49→36.99 Å / Num. all: 14676 / Num. obs: 14676 / % possible obs: 94.5 % / Redundancy: 4.6 % / CC1/2: 0.989 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.045 / Rrim(I) all: 0.095 / Rsym value: 0.083 / Net I/σ(I): 12.2 / Num. measured all: 67485
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRsym value% possible all
2.49-2.6340.1746.2614315180.950.0410.07468.6
7.88-36.994.30.07416.122495220.9890.0380.07294.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.15data extraction
iMOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OW4

2ow4


Resolution: 2.52→36.99 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.896 / WRfactor Rfree: 0.2646 / WRfactor Rwork: 0.1933 / FOM work R set: 0.8091 / SU Rfree: 0.3376 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.338 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2509 754 5.2 %RANDOM
Rwork0.1845 ---
obs0.1879 13883 97.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.02 Å2 / Biso mean: 27.912 Å2 / Biso min: 9.19 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å2-0 Å2
2---0.05 Å20 Å2
3---0.03 Å2
Refinement stepCycle: final / Resolution: 2.52→36.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3588 0 30 98 3716
Biso mean--29.22 24.31 -
Num. residues----473
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193710
X-RAY DIFFRACTIONr_bond_other_d00.023423
X-RAY DIFFRACTIONr_angle_refined_deg1.6631.955063
X-RAY DIFFRACTIONr_angle_other_deg3.80637908
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8955475
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.07924.706153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.59715572
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6291513
X-RAY DIFFRACTIONr_chiral_restr0.090.2589
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214225
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02834
X-RAY DIFFRACTIONr_mcbond_it2.0672.7371891
X-RAY DIFFRACTIONr_mcbond_other2.0632.7361890
X-RAY DIFFRACTIONr_mcangle_it3.444.0972360
LS refinement shellResolution: 2.523→2.589 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 56 -
Rwork0.255 904 -
all-960 -
obs--88.64 %

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