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- PDB-4h55: Crystal structure of Canavalia brasiliensis seed lectin (ConBr) i... -

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Basic information

Entry
Database: PDB / ID: 4h55
TitleCrystal structure of Canavalia brasiliensis seed lectin (ConBr) in complex with beta-d-ribofuranose
ComponentsConcanavalin-Br
KeywordsSUGAR BINDING PROTEIN / Sugar-binding protein / beta-sandwich / Sugar recognition / Carbohydrate-binding protein
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, 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
beta-D-ribofuranose / D-ALPHA-AMINOBUTYRIC ACID / : / Concanavalin-Br
Similarity search - Component
Biological speciesCanavalia brasiliensis (Brazilian jackbean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsSalviano, E. / Rocha, B.A.M. / Cavada, B.S. / Delatorre, P. / Santi-Gadelha, T. / Gadelha, C.A.A. / Silva-Filho, J.C. / Nobrega, R.B. / Farias, D.L.
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of Canavalia brasiliensis seed lectin (ConBr) in complex with beta-d-ribofuranose
Authors: Salviano, E. / Rocha, B.A.M. / Cavada, B.S. / Delatorre, P. / Santi-Gadelha, T. / Gadelha, C.A.A. / Silva-Filho, J.C. / Nobrega, R.B. / Farias, D.L.
History
DepositionSep 18, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionOct 31, 2012ID: 4DPS
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / 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 / struct_conn / 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_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.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 2.1Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
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-Br
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9415
Polymers25,5921
Non-polymers3484
Water1,44180
1
A: Concanavalin-Br
hetero molecules

A: Concanavalin-Br
hetero molecules

A: Concanavalin-Br
hetero molecules

A: Concanavalin-Br
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,76320
Polymers102,3704
Non-polymers1,39316
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area8520 Å2
ΔGint-125 kcal/mol
Surface area32120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.240, 70.430, 97.570
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 / Sugars , 2 types, 2 molecules A

#1: Protein Concanavalin-Br / Con Br


Mass: 25592.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Canavalia brasiliensis (Brazilian jackbean)
References: UniProt: P55915
#4: Sugar ChemComp-BDR / beta-D-ribofuranose / beta-D-ribose / D-ribose / ribose / BETA-D-RIBOFURANOSYL


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
DRibfbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-ribofuranoseCOMMON NAMEGMML 1.0
b-D-RibfIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
RibSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 83 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-DBB / D-ALPHA-AMINOBUTYRIC ACID


Type: D-peptide linking / Mass: 103.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.8 M ammonium sulfate, 0.2 M sodium chloride, 0.1 M HEPES, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.428 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Sep 25, 2006
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.428 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.939
11K, H, -L20.061
ReflectionResolution: 2.15→27.68 Å / Num. all: 135906 / Num. obs: 12586 / % possible obs: 90.75 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1

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Processing

Software
NameVersionClassification
iMOSFLMdata reduction
MOLREPphasing
REFMAC5.5.0110refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→24.39 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.91 / SU B: 10.353 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22657 594 4.6 %RANDOM
Rwork0.18331 ---
obs0.18528 11606 87.79 %-
all-12200 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.553 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20 Å20 Å2
2--0.78 Å20 Å2
3----1.39 Å2
Refinement stepCycle: LAST / Resolution: 2.15→24.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1775 0 19 80 1874
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221831
X-RAY DIFFRACTIONr_angle_refined_deg2.1421.9532492
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.945231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.77224.53375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.35115285
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.463157
X-RAY DIFFRACTIONr_chiral_restr0.1340.2288
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211378
X-RAY DIFFRACTIONr_mcbond_it1.3041.51162
X-RAY DIFFRACTIONr_mcangle_it2.12621879
X-RAY DIFFRACTIONr_scbond_it3.0343669
X-RAY DIFFRACTIONr_scangle_it4.5024.5613
X-RAY DIFFRACTIONr_rigid_bond_restr1.96731831
X-RAY DIFFRACTIONr_sphericity_free7.049383
X-RAY DIFFRACTIONr_sphericity_bonded3.12231792
LS refinement shellResolution: 2.066→2.119 Å / Num. reflection Rfree: 0 / Num. reflection Rwork: 0 / Total num. of bins used: 20

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