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- PDB-1cvn: CONCANAVALIN A COMPLEXED TO TRIMANNOSIDE -

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Basic information

Entry
Database: PDB / ID: 1cvn
TitleCONCANAVALIN A COMPLEXED TO TRIMANNOSIDE
ComponentsCONCANAVALIN A
KeywordsLECTIN (AGGLUTININ) / CONCANAVALIN A / SACCHARIDE BINDING
Function / homology
Function and homology information


regulation of defense response to virus / D-mannose binding / defense response / metal ion binding
Similarity search - Function
Legume lectin / 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 / : / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily ...Legume lectin / 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 / : / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesCanavalia ensiformis (jack bean)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsNaismith, J.H.
Citation
Journal: J.Biol.Chem. / Year: 1996
Title: Structural basis of trimannoside recognition by concanavalin A.
Authors: Naismith, J.H. / Field, R.A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1994
Title: Refined Structure of Concanavalin a Complexed with Methyl Alpha-D-Mannopyranoside at 2.0A Resolution and Comparison with the Saccharide-Free Structure
Authors: Naismith, J.H. / Emmerich, C. / Habash, J. / Harrop, S.J. / Helliwell, J.R. / Hunter, W.N. / Raftery, J. / Kalb(Gilboa), A.J. / Yariv, J.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1993
Title: Refined Structure of Cadmium-Substituted Concanavalin a at 2.0A Resolution
Authors: Naismith, J.H. / Habash, J. / Harrop, S.J. / Helliwell, J.R. / Hunter, W.N. / Wan, T.C.M. / Weisgerber, S. / Kalb(Gilboa), A.J. / Yariv, J.
History
DepositionAug 9, 1995Processing site: BNL
Revision 1.0Oct 14, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Advisory / Data collection / Other
Category: diffrn_detector / pdbx_database_status ...diffrn_detector / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _diffrn_detector.detector / _pdbx_database_status.process_site
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_ref_seq_dif / 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.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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_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.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.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 9, 2023Group: Advisory / Database references ...Advisory / Database references / Refinement description / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)104,88716
Polymers102,4904
Non-polymers2,39812
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13510 Å2
ΔGint-76 kcal/mol
Surface area33130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.650, 66.680, 108.320
Angle α, β, γ (deg.)90.00, 97.79, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.43731, -0.07711, 0.896), (-0.07251, -0.99005, -0.12059), (0.89639, -0.1177, 0.42736)-4.13543, 4.40101, 2.84565
2given(0.43925, -0.01169, -0.89829), (-0.00275, -0.99993, 0.01167), (-0.89836, -0.00266, -0.43925)33.50522, -0.36648, 53.7058
3given(-0.99621, 0.0855, 0.01625), (0.08684, 0.98882, 0.12124), (-0.0057, 0.12219, -0.99249)28.88466, -4.75541, 56.26678

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Components

#1: Protein
CONCANAVALIN A / CON A


Mass: 25622.385 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: TRIMANNOSIDE COMPLEX / Source: (natural) Canavalia ensiformis (jack bean) / References: UniProt: P02866
#2: Polysaccharide
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a1122h-1a_1-5]/1-1-1/a3-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+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


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.85 Å3/Da / Density % sol: 53 %
Crystal growpH: 9 / Details: pH 9.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlprotein1drop
27 mMtrimannoside 1drop
320 %PEG60001reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceWavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Jul 13, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→8 Å / Num. obs: 48025 / % possible obs: 95.54 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.085
Reflection shellResolution: 2.3→2.4 Å / Rmerge(I) obs: 0.222 / % possible all: 80
Reflection shell
*PLUS
% possible obs: 80 % / Redundancy: 1.5 % / Num. unique obs: 5025

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Processing

Software
NameVersionClassification
X-PLOR2.1model building
X-PLOR2.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR2.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CNA

5cna


Resolution: 2.3→8 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.255 4470 10 %
Rwork0.204 --
obs0.204 44380 88.3 %
Displacement parametersBiso mean: 17.96 Å2
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7236 0 144 273 7653
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.781
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.54
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.478
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.54
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.478

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