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- PDB-1apn: THE CRYSTALLOGRAPHIC STRUCTURE OF METAL-FREE CONCANAVALIN A AT 2.... -

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Basic information

Entry
Database: PDB / ID: 1apn
TitleTHE CRYSTALLOGRAPHIC STRUCTURE OF METAL-FREE CONCANAVALIN A AT 2.5 ANGSTROMS RESOLUTION
ComponentsCONCANAVALIN A
KeywordsLECTIN
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 / Jelly Rolls ...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: 2.5 Å
AuthorsBouckaert, J. / Loris, R. / Poortmans, F. / Wyns, L.
Citation
Journal: Proteins / Year: 1995
Title: Crystallographic structure of metal-free concanavalin A at 2.5 A resolution.
Authors: Bouckaert, J. / Loris, R. / Poortmans, F. / Wyns, L.
#1: Journal: J.Mol.Biol. / Year: 1979
Title: Crystal Structure of Demetallized Concanavalin A. The Metal-Binding Region
Authors: Shoham, M. / Yonath, A. / Sussman, J.L. / Moult, J. / Traub, W. / Gilboa(Kalb), A.J.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1978
Title: Changes in the Three-Dimensional Structure of Concanavalin a Upon Demetallization
Authors: Reeke Junior, G.N. / Becker, J.W. / Edelman, G.M.
History
DepositionJul 28, 1995Processing site: BNL
Revision 1.0Apr 3, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)51,2452
Polymers51,2452
Non-polymers00
Water3,027168
1
A: CONCANAVALIN A
B: CONCANAVALIN A

A: CONCANAVALIN A
B: CONCANAVALIN A


Theoretical massNumber of molelcules
Total (without water)102,4904
Polymers102,4904
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)61.360, 85.460, 91.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Atom site foot note1: GLU A 122 - THR A 123 OMEGA = 210.44 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.970545, 0.240787, 0.007974), (0.240796, -0.970576, -0.000182), (0.007696, 0.002096, -0.999968)
Vector: -0.2292, 0.0357, 45.6812)
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 B 1 .. B 237 A 1 .. A 237 0.559

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Components

#1: Protein CONCANAVALIN A / CON A


Mass: 25622.385 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: DEMETALLIZED, PH 5 / Source: (natural) Canavalia ensiformis (jack bean) / References: UniProt: P02866
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.34 Å3/Da / Density % sol: 47.41 %
Crystal
*PLUS
Density % sol: 44 %
Crystal grow
*PLUS
pH: 5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
111 mg/mlprotein1drop
22 Mammonium sulfate1reservoirprecipitant
3100 mMsodium acetate1reservoirprecipitant
45 %PEG60001reservoirprecipitant
5precipitant1drop

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorDetector: AREA DETECTOR / Date: Jan 20, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→15 Å / Num. obs: 16834 / % possible obs: 98 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.078
Reflection
*PLUS
Num. measured all: 88305 / Rmerge(I) obs: 0.078

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MADNESSdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.5→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.247 -10 %
Rwork0.18 --
obs0.18 16601 98 %
Displacement parametersBiso mean: 32 Å2
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3424 0 0 168 3592
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
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_deg3.231
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.51
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.825
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
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.51
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.825

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