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- PDB-1con: THE REFINED STRUCTURE OF CADMIUM SUBSTITUTED CONCANAVALIN A AT 2.... -

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Entry
Database: PDB / ID: 1con
TitleTHE REFINED STRUCTURE OF CADMIUM SUBSTITUTED CONCANAVALIN A AT 2.0 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, beta chain, Mn/Ca-binding site / Legume lectin domain / : / 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, 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 ensiformis (jack bean)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsNaismith, J.H. / Habash, J. / Harrop, S.J. / Helliwell, J.R. / Hunter, W.N. / Kalb(Gilboa), A.J. / Yariv, J. / Wan, T.C.M. / Weisgerber, S.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1993
Title: Refined structure of cadmium-substituted concanavalin A at 2.0 A resolution.
Authors: Naismith, J.H. / Habash, J. / Harrop, S. / Helliwell, J.R. / Hunter, W.N. / Wan, T.C. / Weisgerber, S. / Kalb, A.J. / Yariv, J.
#1: Journal: Embo J. / Year: 1992
Title: Non-Glycosylated Recombinant Pro-Concanavalin a is Active without Polypeptide Cleavage
Authors: Min, W. / Dunn, A.J. / Jones, D.H.
History
DepositionMar 16, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET THE MOST STRIKING FEATURE OF CONCANAVALIN A IS TWO LARGE BETA SHEETS IN THE STRUCTURE ...SHEET THE MOST STRIKING FEATURE OF CONCANAVALIN A IS TWO LARGE BETA SHEETS IN THE STRUCTURE COMPRISING 111 OF THE 237 AMINO ACIDS. THERE IS NO ALPHA HELIX. THE REMAINING AMINO ACIDS FORM A SERIES OF LOOPS AND TURNS. THE PURPOSE OF THIS STUDY IS TO PROVIDE A WELL-REFINED SACCHARIDE-FREE STRUCTURE BASED UPON THE CORRECTED AMINO ACID SEQUENCE. THIS STRUCTURE IS PART OF A BROADER STUDY TO DEFINE THE PROTEIN SACCHARIDE INTERACTIONS OF CONCANAVALIN A.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CONCANAVALIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8874
Polymers25,6221
Non-polymers2653
Water2,594144
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)103,54916
Polymers102,4904
Non-polymers1,06012
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 area11230 Å2
ΔGint-149 kcal/mol
Surface area32080 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)88.700, 86.500, 62.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Atom site foot note1: ALA A 207 - ASP A 208 OMEGA = 0.16 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: THE FOLLOWING SURFACE LOOPS ARE IN WEAK DENSITY: A 118 - A 123, A 149 - A 152, AND A 159 - A 162.
Components on special symmetry positions
IDModelComponents
11A-384-

HOH

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Components

#1: Protein CONCANAVALIN A


Mass: 25622.385 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canavalia ensiformis (jack bean) / Organ: BEAN / References: UniProt: P02866
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#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.: 144 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE AUTHORS STATE THAT THIS IS THE CORRECT AMINO ACID SEQUENCE FOR CONCANAVALIN A, ACCORDING TO THE ...THE AUTHORS STATE THAT THIS IS THE CORRECT AMINO ACID SEQUENCE FOR CONCANAVALIN A, ACCORDING TO THE LATEST GENE SEQUENCE. SEE REFERENCE 1 ABOVE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.4 %
Crystal grow
*PLUS
Method: other / Details: Kalb, A.J., (1988) J. Crystal Growth, 88, 537.

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 8 Å / Num. obs: 16178 / % possible obs: 99.1 % / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.1 Å / Num. unique obs: 2188 / Rmerge(I) obs: 0.113

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Processing

Software
NameVersionClassification
X-PLOR2.1model building
X-PLOR2.1refinement
X-PLOR2.1phasing
RefinementResolution: 2→8 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.171 -
obs0.171 16178
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1809 0 3 144 1956
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg2.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.2
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
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 8 Å / Num. reflection all: 16178 / σ(F): 0 / Rfactor all: 0.171
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d2.9
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg1.2

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