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- PDB-1cav: THE THREE-DIMENSIONAL STRUCTURE OF CANAVALIN FROM JACK BEAN (CANA... -

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Basic information

Entry
Database: PDB / ID: 1cav
TitleTHE THREE-DIMENSIONAL STRUCTURE OF CANAVALIN FROM JACK BEAN (CANAVALIA ENSIFORMIS)
Components(CANAVALIN) x 2
KeywordsSEED STORAGE PROTEIN
Function / homology
Function and homology information


nutrient reservoir activity / protein-containing complex / identical protein binding
Similarity search - Function
: / Cupin / Cupin 1 / Cupin / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesCanavalia ensiformis (jack bean)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsKo, T-P. / Ng, J.D. / McPherson, A.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1993
Title: Determination of three crystal structures of canavalin by molecular replacement.
Authors: Ko, T.P. / Ng, J.D. / Day, J. / Greenwood, A. / McPherson, A.
#1: Journal: Plant Physiol. / Year: 1993
Title: The three-dimensional structure of canavalin from jack bean (Canavalia ensiformis).
Authors: Ko, T.-P. / Ng, J.D. / Day, J. / Greenwood, A. / McPherson, A.
History
DepositionMay 27, 1993Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 4, 2013Group: Database references
Revision 1.4Feb 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CANAVALIN
B: CANAVALIN


Theoretical massNumber of molelcules
Total (without water)41,6102
Polymers41,6102
Non-polymers00
Water00
1
A: CANAVALIN
B: CANAVALIN

A: CANAVALIN
B: CANAVALIN

A: CANAVALIN
B: CANAVALIN


Theoretical massNumber of molelcules
Total (without water)124,8296
Polymers124,8296
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area26970 Å2
ΔGint-160 kcal/mol
Surface area40220 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)126.350, 126.350, 51.640
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein CANAVALIN


Mass: 20968.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canavalia ensiformis (jack bean) / References: UniProt: P50477
#2: Protein CANAVALIN


Mass: 20641.021 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canavalia ensiformis (jack bean) / References: UniProt: P50477

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 56.97 %
Crystal grow
*PLUS
Temperature: 4, 8 ℃ / pH: 6.8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
130-40 mg/mlprotein1drop
22.0 %1reservoirNaCl
30.05 Mphosphate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 2.6→8 Å / σ(I): 3 /
RfactorNum. reflection
obs0.188 10876
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2930 0 0 0 2930
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.02
X-RAY DIFFRACTIONt_angle_deg2.97
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.9
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg24.92
X-RAY DIFFRACTIONt_plane_restr0.019

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