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- PDB-6v7g: Binding of Benzoic Acid and Anions Within the Cupin Domains of th... -

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Basic information

Entry
Database: PDB / ID: 6v7g
TitleBinding of Benzoic Acid and Anions Within the Cupin Domains of the Vicillin Protein Canavalin from Jack Bean (canavalia ensiformis): Crystal Structures
ComponentsCanavalin
KeywordsPLANT PROTEIN / plant proteins / ligands / salicylic acid / enzymes
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 / RmlC-like jelly roll fold
Similarity search - Domain/homology
ACETATE ION / BENZOIC ACID / CITRIC ACID / Canavalin
Similarity search - Component
Biological speciesCanavalia ensiformis (jack bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsMcPherson, A.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Binding of benzoic acid and anions within the cupin domains of the vicilin protein canavalin from jack bean (Canavalia ensiformis): Crystal structures.
Authors: McPherson, A.
History
DepositionDec 8, 2019Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 19, 2020ID: 6CB4
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Canavalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8054
Polymers50,4311
Non-polymers3733
Water4,918273
1
A: Canavalin
hetero molecules

A: Canavalin
hetero molecules

A: Canavalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,41412
Polymers151,2943
Non-polymers1,1209
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-y+2,x-y+2,z1
crystal symmetry operation3_575-x+y,-x+2,z1
Buried area18850 Å2
ΔGint-77 kcal/mol
Surface area39510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.806, 125.806, 49.875
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Canavalin


Mass: 50431.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canavalia ensiformis (jack bean) / References: UniProt: P50477
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.3 Å3/Da / Density % sol: 46 % / Description: short hexagonal prisms
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Vapor diffusion in sitting drop Cryschem plates. Reservoirs were 1.0 M sodium citrate titrated with acetic acid to pH6.0. Drops were initially equal amounts of the reservoir solution with a ...Details: Vapor diffusion in sitting drop Cryschem plates. Reservoirs were 1.0 M sodium citrate titrated with acetic acid to pH6.0. Drops were initially equal amounts of the reservoir solution with a protein stock solution of 30 mg/ml canavalin in water with a trace of ammonium hydroxide. At room temperature crystallization time was about three weeks.
PH range: 5.8 - 6.5

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Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Jun 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→109 Å / Num. obs: 86853 / % possible obs: 99.6 % / Redundancy: 61 % / Biso Wilson estimate: 14.6 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.258 / Rpim(I) all: 0.029 / Rrim(I) all: 0.26 / Rsym value: 0.248 / Net I/σ(I): 18.7
Reflection shellResolution: 1.4→1.43 Å / Redundancy: 11.8 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 3978 / CC1/2: 0.182 / % possible all: 92.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CB4

6cb4
PDB Unreleased entry


Resolution: 1.4→109 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.967 / SU B: 2.607 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.049 / ESU R Free: 0.053
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.188 4348 4.9 %RANDOM
Rwork0.1601 ---
obs0.1614 84484 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 120.09 Å2 / Biso mean: 28.707 Å2 / Biso min: 15.02 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å2-0.33 Å20 Å2
2---0.66 Å20 Å2
3---2.16 Å2
Refinement stepCycle: final / Resolution: 1.4→109 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2873 0 39 275 3187
Biso mean--26.91 42.25 -
Num. residues----357
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133088
X-RAY DIFFRACTIONr_bond_other_d00.0172828
X-RAY DIFFRACTIONr_angle_refined_deg1.5791.6464213
X-RAY DIFFRACTIONr_angle_other_deg1.4271.5736616
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6115393
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.223.333186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.79415550
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.8131522
X-RAY DIFFRACTIONr_chiral_restr0.0810.2391
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023507
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02627
LS refinement shellResolution: 1.4→1.436 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 303 -
Rwork0.376 6222 -
all-6525 -
obs--99.95 %
Refinement TLS params.Method: refined / Origin x: 21.2274 Å / Origin y: 151.639 Å / Origin z: 1.1447 Å
111213212223313233
T0.0217 Å2-0.0224 Å2-0.0115 Å2-0.0366 Å2-0.006 Å2--0.0355 Å2
L0.2276 °20.1173 °2-0.0075 °2-0.8327 °20.017 °2--0.0037 °2
S0.0086 Å °0.0086 Å °-0.006 Å °0.0231 Å °0.0002 Å °-0.0787 Å °-0.0046 Å °0.0094 Å °-0.0088 Å °

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