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- PDB-1dgw: Structure of the rhombohedral crystal of canavalin from jack bean -

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Basic information

Entry
Database: PDB / ID: 1dgw
TitleStructure of the rhombohedral crystal of canavalin from jack bean
Components(CANAVALIN) x 3
KeywordsPLANT PROTEIN / DUPLICATED SWISS-ROLL BETA BARRELS / LOOPS WITH ALPHA HELICES / MEROHEDRAL/ HEMIHEDRAL TWINNING
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 / Jelly Rolls ...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: 1.7 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 26, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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

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Assembly

Deposited unit
A: CANAVALIN
X: CANAVALIN
Y: CANAVALIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0784
Polymers39,9833
Non-polymers951
Water5,260292
1
A: CANAVALIN
X: CANAVALIN
Y: CANAVALIN
hetero molecules

A: CANAVALIN
X: CANAVALIN
Y: CANAVALIN
hetero molecules

A: CANAVALIN
X: CANAVALIN
Y: CANAVALIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,23412
Polymers119,9499
Non-polymers2853
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area45610 Å2
ΔGint-291 kcal/mol
Surface area38050 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)136.876, 136.876, 76.004
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein CANAVALIN /


Mass: 20640.342 Da / Num. of mol.: 1 / 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.: 1 / 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.: 1 / 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 / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 4

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Sample preparation

CrystalDensity Matthews: 3.43 Å3/Da / Density % sol: 64.11 %
Crystal growTemperature: 293 K / Method: liquid diffusion / pH: 6.8
Details: DULBECCO'S PHOSPHATE BUFFERED SALINE, AMMONIUM HYDROXIDE (TRACE), MICROGRAVITY, pH 6.8, LIQUID DIFFUSION, temperature 293K
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: Aug 23, 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.69→300 Å / Num. all: 56649 / Num. obs: 56649 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 27.2 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 18.7
Reflection shellResolution: 1.69→1.78 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.304 / % possible all: 81.1
Reflection
*PLUS
Lowest resolution: 300 Å / Num. measured all: 343806 / Rmerge(I) obs: 0.0885
Reflection shell
*PLUS
% possible obs: 81.1 % / Num. unique obs: 6947 / Num. measured obs: 16233 / Mean I/σ(I) obs: 1.05

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Processing

Software
NameClassification
SDMSdata collection
SDMSdata reduction
MERLOTphasing
CNSrefinement
SDMSdata scaling
RefinementResolution: 1.7→300 Å / σ(F): 2 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER / Details: THE REFINEMENT USED A TWIN FRACTION OF 0.426.
RfactorNum. reflection% reflectionSelection details
Rfree0.252 3869 -RANDOM
Rwork0.189 ---
all0.196 55919 --
obs0.192 48927 83.7 %-
Refinement stepCycle: LAST / Resolution: 1.7→300 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2782 0 5 292 3079
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007132
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.44828
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 500 Å / Num. reflection obs: 49983 / σ(F): 2 / % reflection Rfree: 8 % / Rfactor Rfree: 0.245 / Rfactor Rwork: 0.176
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_deg0.924
LS refinement shell
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 1.78 Å / Rfactor Rfree: 0.386 / Rfactor Rwork: 0.375 / Num. reflection obs: 4062

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