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- PDB-3cna: STRUCTURE OF CONCANAVALIN A AT 2.4 ANGSTROMS RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 3cna
TitleSTRUCTURE OF CONCANAVALIN A AT 2.4 ANGSTROMS RESOLUTION
ComponentsCONCANAVALIN A
KeywordsLECTIN (AGGLUTININ)
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 / Resolution: 2.4 Å
AuthorsHardman, K.D. / Ainsworth, C.F.
Citation
Journal: Biochemistry / Year: 1972
Title: Structure of concanavalin A at 2.4-A resolution.
Authors: Hardman, K.D. / Ainsworth, C.F.
#1: Journal: Biochemistry / Year: 1976
Title: Structure of the Concanavalin A-Methyl-Alpha-D-Mannopyranoside Complex at 6.0 Angstroms Resolution
Authors: Hardman, K.D. / Ainsworth, C.F.
#2: Journal: Biochemistry / Year: 1973
Title: Binding of Nonpolar Molecules by Crystalline Concanavalin A
Authors: Hardman, K.D. / Ainsworth, C.F.
#3: Journal: Adv.Exp.Med.Biol. / Year: 1973
Title: Crystallography of a Metal-Containing Protein, Concanavalin A
Authors: Hardman, K.D.
#4: Journal: Atlas of Macromolecular Structure on Microfiche / Year: 1976
#5: Journal: Atlas of Protein Sequence and Structure,Supplement 2
Year: 1976
History
DepositionSep 15, 1976Processing site: BNL
Revision 1.0Oct 11, 1976Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CONCANAVALIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6913
Polymers25,5961
Non-polymers952
Water724
1
A: CONCANAVALIN A
hetero molecules

A: CONCANAVALIN A
hetero molecules

A: CONCANAVALIN A
hetero molecules

A: CONCANAVALIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,76512
Polymers102,3854
Non-polymers3808
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)63.150, 86.910, 89.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Atom site foot note1: THESE RESIDUES (187-190) ARE ORDERED IN THIS COORDINATE SET TO REFLECT BEST AGREEMENT WITH THE ELECTRON DENSITY. THIS REGION WAS AMBIGUOUS IN THE CHEMICAL DETERMINATION OF THE PRIMARY STRUCTURE.

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Components

#1: Protein CONCANAVALIN A


Mass: 25596.299 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canavalia ensiformis (jack bean) / References: UniProt: P02866
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.39 Å3/Da / Density % sol: 48.56 %
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: batch method
Details: referred to 'Hardman, K.D.', (1971) Proc.Nat.Acad.Sci.U.S., 64. 1393-1397
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mM11MnCl2
210 mM11CaCl2
34 Msodium phosphate12

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Data collection

Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 6 Å / Num. obs: 10000 / Observed criterion σ(I): 2 / Num. measured all: 90000

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Processing

RefinementHighest resolution: 2.4 Å
Refinement stepCycle: LAST / Highest resolution: 2.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1807 0 2 4 1813
Refinement
*PLUS
Highest resolution: 2.4 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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