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- PDB-1dgr: Refined crystal structure of canavalin from jack bean -

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Basic information

Entry
Database: PDB / ID: 1dgr
TitleRefined crystal structure of canavalin from jack bean
Components(CANAVALIN) x 3
KeywordsPLANT PROTEIN / DUPLICATED DOMAINS BETA BARREL HELICAL LOOP
Function / homology
Function and homology information


nutrient reservoir activity / protein-containing complex / identical protein binding
Similarity search - Function
Arc Repressor Mutant, subunit A - #840 / Jelly Rolls - #1450 / : / Cupin / Cupin 1 / Cupin / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Arc Repressor Mutant, subunit A ...Arc Repressor Mutant, subunit A - #840 / Jelly Rolls - #1450 / : / Cupin / Cupin 1 / Cupin / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Arc Repressor Mutant, subunit A / Jelly Rolls / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Canavalin
Similarity search - Component
Biological speciesCanavalia ensiformis (jack bean)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsKo, T.-P. / McPherson, A.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: X-ray diffraction and atomic force microscopy analysis of twinned crystals: rhombohedral canavalin.
Authors: Ko, T.P. / Kuznetsov, Y.G. / Malkin, A.J. / Day, J. / McPherson, A.
#1: 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.
History
DepositionNov 25, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CANAVALIN
X: CANAVALIN
Y: CANAVALIN
B: CANAVALIN
V: CANAVALIN
W: CANAVALIN
C: CANAVALIN
N: CANAVALIN
M: CANAVALIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,23412
Polymers119,9499
Non-polymers2853
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area46100 Å2
ΔGint-300 kcal/mol
Surface area36000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.5, 150.3, 133.4
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number20
Space group name H-MC2221
DetailsThe trimeric assembly contains three identical subunits of chains A,X,Y; B,V,W; and C,N,M.

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Components

#1: Protein CANAVALIN


Mass: 20640.342 Da / Num. of mol.: 3 / Fragment: RESIDUES 46-223 / Source method: isolated from a natural source
Details: LEGUME STORAGE PROTEIN; LIMITED DIGESTION BY TRYPSIN
Source: (natural) Canavalia ensiformis (jack bean) / Organ: SEED / Tissue: COTYLEDON / References: UniProt: P50477
#2: Protein CANAVALIN


Mass: 9073.182 Da / Num. of mol.: 3 / Fragment: RESIDUES 246-324 / Source method: isolated from a natural source
Details: LEGUME STORAGE PROTEIN; LIMITED DIGESTION BY TRYPSIN
Source: (natural) Canavalia ensiformis (jack bean) / Organ: SEED / Tissue: COTYLEDON / References: UniProt: P50477
#3: Protein CANAVALIN


Mass: 10269.446 Da / Num. of mol.: 3 / Fragment: RESIDUES 331-423 / Source method: isolated from a natural source
Details: LEGUME STORAGE PROTEIN; LIMITED DIGESTION BY TRYPSIN
Source: (natural) Canavalia ensiformis (jack bean) / Organ: SEED / Tissue: COTYLEDON / References: UniProt: P50477
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: Dulbeccos phosphate buffered saline, ammonium hydroxide, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Details: Koszelak, S., (1995) Biophys. J., 69, 13.

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SDMS / Detector: AREA DETECTOR / Date: Jan 23, 1989
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→200 Å / Num. all: 42478 / Num. obs: 37938 / % possible obs: 89.3 % / Redundancy: 3.7 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.0548 / Net I/σ(I): 21.3
Reflection shellResolution: 2.6→2.8 Å / Redundancy: 2.58 % / Rmerge(I) obs: 0.1744 / Num. unique all: 7058 / % possible all: 83

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Processing

Software
NameClassification
SDMSdata collection
SDMSdata reduction
MERLOTphasing
CNSrefinement
SDMSdata scaling
RefinementResolution: 2.6→200 Å / σ(F): 3 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Strong NCS restraints were used.
RfactorNum. reflection% reflectionSelection details
Rfree0.226 2307 -Random
Rwork0.18 ---
all0.201 42478 --
obs0.184 28811 67.8 %-
Refinement stepCycle: LAST / Resolution: 2.6→200 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8347 0 15 168 8530
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4312
X-RAY DIFFRACTIONc_bond_d0.00744
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 500 Å / σ(F): 3 / Rfactor obs: 0.181 / Rfactor Rwork: 0.18 / % reflection Rfree: 8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.808
LS refinement shell
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 2.76 Å / Rfactor Rfree: 0.263 / Rfactor Rwork: 0.23 / Num. reflection obs: 2283

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