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- PDB-2cav: CANAVALIN FROM JACK BEAN -

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Basic information

Entry
Database: PDB / ID: 2cav
TitleCANAVALIN FROM JACK BEAN
ComponentsPROTEIN (CANAVALIN)
KeywordsPLANT PROTEIN / VICILIN / 7S SEED PROTEIN / DOMAIN DUPLICATION / SWISS ROLL
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 / MIR / Resolution: 2 Å
AuthorsKo, T.-P. / Day, J. / Macpherson, A.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: The refined structure of canavalin from jack bean in two crystal forms at 2.1 and 2.0 A resolution.
Authors: Ko, T.P. / Day, J. / 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. / Macpherson, A.
History
DepositionNov 20, 1998Processing site: RCSB
Revision 1.0Nov 25, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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: PROTEIN (CANAVALIN)


Theoretical massNumber of molelcules
Total (without water)50,3831
Polymers50,3831
Non-polymers00
Water2,954164
1
A: PROTEIN (CANAVALIN)

A: PROTEIN (CANAVALIN)

A: PROTEIN (CANAVALIN)


Theoretical massNumber of molelcules
Total (without water)151,1503
Polymers151,1503
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area14300 Å2
ΔGint-100 kcal/mol
Surface area39010 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)126.430, 126.430, 51.370
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 PROTEIN (CANAVALIN) / JACK BEAN VICILIN


Mass: 50383.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: TREATED WITH LIMITED DIGESTION BY TRYPSIN / Source: (natural) Canavalia ensiformis (jack bean) / Cellular location: PROTEIN BODY / Organ: SEED / Tissue: COTYLEDON / References: UniProt: P50477
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 48 % / Description: REFERENCE TO PDB1CAV
Crystal growMethod: vapor diffusion / pH: 6.8
Details: 30 - 40 MG/ML PROTEIN SOLUTION WAS PREPARED BY DISSOLVING 4-TIME RECRYSTALLIZED CANAVALIN IN DISTILLED WATER PLUS TRACE NH4OH. RESERVOIR SOLUTION CONTAINED 2.0 % NACL IN 50 MM PHOSPHATE ...Details: 30 - 40 MG/ML PROTEIN SOLUTION WAS PREPARED BY DISSOLVING 4-TIME RECRYSTALLIZED CANAVALIN IN DISTILLED WATER PLUS TRACE NH4OH. RESERVOIR SOLUTION CONTAINED 2.0 % NACL IN 50 MM PHOSPHATE BUFFER AT PH 6.8. CRYSTALS WERE OBTAINED BY MIXING PROTEIN AND RESERVOIR SOLUTION IN SITTING DROPS FOLLOWED BY VAPOR DIFFUSION AGAINST THE RESERVOIR., vapor diffusion
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 277-281 K / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115-20 mg/mlprotein1drop
21.0 %1dropNaCl
350 mMphosphate1drop

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SDMS / Detector: AREA DETECTOR / Date: Aug 1, 1994
RadiationMonochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 31848 / % possible obs: 99.7 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 24
Reflection shellResolution: 2→2.15 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.312 / Mean I/σ(I) obs: 3.4 / % possible all: 99.6
Reflection
*PLUS
Num. measured all: 337907
Reflection shell
*PLUS
% possible obs: 99.6 % / Num. unique obs: 6302 / Num. measured obs: 29912

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Processing

Software
NameVersionClassification
X-PLOR3.8refinement
SDMSdata reduction
SDMSdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2→40 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.264 2510 8 %RANDOM
Rwork0.208 ---
obs0.208 30894 96.7 %-
Displacement parametersBiso mean: 37.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.27 Å
Luzzati d res low-40 Å
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2781 0 0 164 2945
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_deg1.707
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.72
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.812
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.421.5
X-RAY DIFFRACTIONx_mcangle_it2.442
X-RAY DIFFRACTIONx_scbond_it2.242
X-RAY DIFFRACTIONx_scangle_it3.542.5
LS refinement shellResolution: 2→2.07 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.37 219 6.9 %
Rwork0.333 2428 -
obs--83.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2TOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.54 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 37.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.72
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.812
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.37 / % reflection Rfree: 6.9 % / Rfactor Rwork: 0.333 / Num. reflection obs: 2647 / Rfactor obs: 0.333

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