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- PDB-5cna: REFINED STRUCTURE OF CONCANAVALIN A COMPLEXED WITH ALPHA-METHYL-D... -

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Entry
Database: PDB / ID: 5cna
TitleREFINED STRUCTURE OF CONCANAVALIN A COMPLEXED WITH ALPHA-METHYL-D-MANNOPYRANOSIDE AT 2.0 ANGSTROMS RESOLUTION AND COMPARISON WITH THE SACCHARIDE-FREE STRUCTURE
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
methyl alpha-D-mannopyranoside / : / Concanavalin-A
Similarity search - Component
Biological speciesCanavalia ensiformis (jack bean)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsNaismith, J.H. / Emmerich, C. / Habash, J. / Harrop, S.J. / Helliwell, J.R. / Hunter, W.N. / Raftery, J. / Kalb(Gilboa), A.J. / Yariv, J.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1994
Title: Refined structure of concanavalin A complexed with methyl alpha-D-mannopyranoside at 2.0 A 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, A.J. / Yariv, J.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1994
Title: High-Resolution Structures of Single-Metal-Substituted Concanavalin A: The Co,Ca-Protein at 1.6 Angstroms and the Ni,Ca-Protein at 2.0 Angstroms
Authors: Emmerich, C. / Helliwell, J.R. / Redshaw, M. / Naismith, J.H. / Harrop, S.J. / Raftery, J. / Kalb(Gilboa), A.J. / Yariv, J. / Dauter, Z. / Wilson, K.S.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1993
Title: Refined Structure of Cadmium-Substituted Concanavalin a at 2.0 Angstroms Resolution
Authors: Naismith, J.H. / Habash, J. / Harrop, S. / Helliwell, J.R. / Hunter, W.N. / Wan, T.C.M. / Weisgerber, S. / Kalb(Gilboa), A.J. / Yariv, J.
#3: Journal: J.Chem.Soc.,Faraday Trans. / Year: 1993
Title: High-Resolution Crystallographic Studies of Native Concanavalin a Using Rapid Laue Data Collection Methods and the Introduction of a Monochromatic Large-Angle Oscillation Technique (Lot)
Authors: Weisgerber, S. / Helliwell, J.R.
#4: Journal: Embo J. / Year: 1992
Title: Non-Glycosylated Recombinant Pro-Concanavalin a is Active without Polypeptide Cleavage
Authors: Min, W. / Dunn, A.J. / Jones
#5: Journal: Embo J. / Year: 1989
Title: The Structure of the Saccharide Binding-Site of Concanavalin A
Authors: Derewenda, Z. / Yariv, J. / Helliwell, J.R. / Kalb(Gilboa), A.J. / Dodson, E.J. / Papiz, M.Z. / Wan, T. / Campbell, J.
History
DepositionFeb 11, 1994Processing site: BNL
SupersessionMay 31, 1994ID: 4CNA
Revision 1.0May 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.process_site / _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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Mar 6, 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

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)103,68217
Polymers102,4904
Non-polymers1,19213
Water9,602533
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11320 Å2
ΔGint-101 kcal/mol
Surface area32660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.700, 128.600, 67.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: ALA A 207 - ASP A 208 OMEGA = 0.18 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: ALA B 207 - ASP B 208 OMEGA =359.31 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
3: ALA C 207 - ASP C 208 OMEGA = 0.18 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
4: ALA D 207 - ASP D 208 OMEGA = 1.05 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
5: THE ATOMS LABELLED OD1 AND OD2 IN ASP 10 OF EACH SUBUNIT HAVE BEEN INTERCHANGED COMPARED WITH THE LABELS IN THE PUBLISHED PAPERS.

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Components

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
CONCANAVALIN A


Mass: 25622.385 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canavalia ensiformis (jack bean) / Gene: CDNA / Organ: BEAN / References: UniProt: P02866
#2: Sugar
ChemComp-MMA / methyl alpha-D-mannopyranoside / O1-METHYL-MANNOSE / methyl alpha-D-mannoside / methyl D-mannoside / methyl mannoside


Type: D-saccharide / Mass: 194.182 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C7H14O6
IdentifierTypeProgram
DManp[1Me]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-a-D-mannopyranoseCOMMON NAMEGMML 1.0
o1-methyl-mannoseIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 542 molecules

#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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 533 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE SEQUENCE HAS NOT BEEN REPORTED. IT WAS DERIVED FROM THE CDNA SEQUENCE OF MIN ET AL., 1992, ...THE SEQUENCE HAS NOT BEEN REPORTED. IT WAS DERIVED FROM THE CDNA SEQUENCE OF MIN ET AL., 1992, LISTED AS REFERENCE 3 ABOVE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.81 %
Crystal grow
*PLUS
pH: 6.8 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
180-150 mg/mlprotein11
20.05 MPIPES12
30.1 M12NaNO3
41 mM12MnCl2
51 mM12CaCl2
62 mg/ml12NaN3
70.1 Mmethyl alpha-D-mannopyranoside12

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Data collection

Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 8 Å / Num. obs: 58871 / % possible obs: 82 % / Observed criterion σ(F): 1 / Num. measured all: 62198 / Rmerge(I) obs: 0.076

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Processing

Software
NameVersionClassification
X-PLOR2.1model building
X-PLOR2.1refinement
X-PLOR2.1phasing
RefinementResolution: 2→8 Å / σ(F): 1
Details: THE THREE RAMACHANDRAN OUTLIERS THR A 120, HIS A 121 AND SER B 204) DESCRIBED IN NAISMITH ET AL. ARE IN POORLY DEFINED REGIONS OF ELECTRON DENSITY.
RfactorNum. reflection
Rwork0.199 -
obs0.199 58871
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7236 0 61 533 7830
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg3.15
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.26
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: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 32 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d3.15
X-RAY DIFFRACTIONx_dihedral_angle_d26.989
X-RAY DIFFRACTIONx_dihedral_angle_deg1.26

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