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- PDB-2p34: Crystal structure of a lectin from Canavalia maritima seeds (CML)... -

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Basic information

Entry
Database: PDB / ID: 2p34
TitleCrystal structure of a lectin from Canavalia maritima seeds (CML) in complex with man1-4man-OMe
ComponentsLectin
KeywordsPLANT PROTEIN / Canavalia maritima lectin / dimannoside
Function / homology
Function and homology information


D-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
Biological speciesCanavalia maritima (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMoreno, F.B.M.B. / Bezerra, G.A. / Oliveira, T.M. / Souza, E.P. / Rocha, B.A.M. / Benevides, R.G. / Delatorre, P. / Cavada, B.S. / de Azevedo Jr., W.
CitationJournal: J.Struct.Biol. / Year: 2007
Title: Structural analysis of Canavalia maritima and Canavalia gladiata lectins complexed with different dimannosides: new insights into the understanding of the structure-biological activity ...Title: Structural analysis of Canavalia maritima and Canavalia gladiata lectins complexed with different dimannosides: new insights into the understanding of the structure-biological activity relationship in legume lectins.
Authors: Bezerra, G.A. / Oliveira, T.M. / Moreno, F.B.M.B. / de Souza, E.P. / da Rocha, B.A.M. / Benevides, R.G. / Delatorre, P. / de Azevedo Jr., W.F. / Cavada, B.S.
History
DepositionMar 8, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_validate_chiral / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 21, 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
Remark 999SEQUENCE NO SUITABLE SEQUENCE DATABASE REFERENCE WAS AVAIALBLE AT THE TIME OF PROCESSING THIS ENTRY.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lectin
B: Lectin
C: Lectin
D: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,78216
Polymers101,9774
Non-polymers1,80512
Water8,017445
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10510 Å2
ΔGint-94 kcal/mol
Surface area32060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.446, 69.446, 161.454
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
Lectin /


Mass: 25494.195 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: seed protein / Source: (natural) Canavalia maritima (plant) / References: UniProt: P81364
#2: Polysaccharide
alpha-D-mannopyranose-(1-4)-methyl alpha-D-mannopyranoside


Type: oligosaccharide / Mass: 356.323 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DManp[1Me]a1-OMEGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a1122h-1a_1-5_1*OC][a1122h-1a_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][b-D-Manp]{[(4+1)][a-D-Manp]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 445 / 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: 2.2 Å3/Da / Density % sol: 44.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 4.5 - 6.5 sodium formate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.438 Å
DetectorType: MAR CCD 130 mm / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.438 Å / Relative weight: 1
ReflectionResolution: 2.1→33.52 Å / Num. obs: 49112 / Redundancy: 5.2 % / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 15.6
Reflection shellResolution: 2.1→2.155 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.348 / Rsym value: 0.39

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→33.52 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.909 / SU B: 5.08 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.262 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2392 2489 5.1 %RANDOM
Rwork0.1749 ---
obs0.17815 46558 96.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.194 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→33.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7106 0 104 445 7655
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0227362
X-RAY DIFFRACTIONr_angle_refined_deg2.1431.95710036
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.4545928
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.75524.834302
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.22151130
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1231524
X-RAY DIFFRACTIONr_chiral_restr0.1570.21180
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025500
X-RAY DIFFRACTIONr_nbd_refined0.2390.24055
X-RAY DIFFRACTIONr_nbtor_refined0.3170.25093
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.2646
X-RAY DIFFRACTIONr_metal_ion_refined0.1290.223
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2640.2107
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2250.233
X-RAY DIFFRACTIONr_mcbond_it1.0651.54687
X-RAY DIFFRACTIONr_mcangle_it1.81927512
X-RAY DIFFRACTIONr_scbond_it2.85932974
X-RAY DIFFRACTIONr_scangle_it4.0784.52524
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 168 -
Rwork0.19 3347 -
obs--94.8 %

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