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- PDB-6v7l: The structure of the P212121 crystal form of canavalin at 173 K -

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Basic information

Entry
Database: PDB / ID: 6v7l
TitleThe structure of the P212121 crystal form of canavalin at 173 K
ComponentsCanavalin
KeywordsPLANT PROTEIN / precanavalin / proteolytic cleavage / vicillim / storage protein / benzoic acid
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
BENZOIC ACID / Canavalin
Similarity search - Component
Biological speciesCanavalia ensiformis (jack bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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
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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Canavalin
B: Canavalin
C: Canavalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,5176
Polymers151,1503
Non-polymers3663
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assembled in the plant seed
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15860 Å2
ΔGint-81 kcal/mol
Surface area39630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.889, 90.511, 183.739
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 46 - 424 / Label seq-ID: 46 - 424

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Canavalin


Mass: 50383.469 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canavalia ensiformis (jack bean) / Production host: Canavalia ensiformis (jack bean) / References: UniProt: P50477
#2: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.43 Å3/Da / Density % sol: 49 % / Description: elongated regtangular prisms
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Crystals were grown by sitting drop vapor diffusion from 18% PEG 3350 in 0.1 M HEPES reservoirs. The drops were equal amounts of a 40 mg/ml solution of precanavalin (not treated with any ...Details: Crystals were grown by sitting drop vapor diffusion from 18% PEG 3350 in 0.1 M HEPES reservoirs. The drops were equal amounts of a 40 mg/ml solution of precanavalin (not treated with any exogenous protease) in water. Crystals grew only after six to eight weeks at room temperature.
PH range: 7.0 - 7.8

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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: 2.75→60 Å / Num. obs: 28813 / % possible obs: 73.4 % / Redundancy: 17.2 % / Biso Wilson estimate: 54 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.282 / Rpim(I) all: 0.07 / Rrim(I) all: 0.29 / Rsym value: 0.275 / Net I/σ(I): 9.9
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 0.4 / Num. unique obs: 2131 / CC1/2: 0.025 / % possible all: 8.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CAX

1cax


Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.904 / SU B: 51.145 / SU ML: 0.386 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.438 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1442 5.1 %RANDOM
Rwork0.1933 ---
obs0.1962 27012 78.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 240.45 Å2 / Biso mean: 78.346 Å2 / Biso min: 21.76 Å2
Baniso -1Baniso -2Baniso -3
1--1.59 Å20 Å20 Å2
2---1.34 Å20 Å2
3---2.93 Å2
Refinement stepCycle: final / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8406 0 42 83 8531
Biso mean--102.43 62.9 -
Num. residues----1046
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0138649
X-RAY DIFFRACTIONr_bond_other_d00.0177989
X-RAY DIFFRACTIONr_angle_refined_deg1.2851.64511714
X-RAY DIFFRACTIONr_angle_other_deg1.1281.57318591
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.42451052
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.97823.023516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.143151519
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1911563
X-RAY DIFFRACTIONr_chiral_restr0.0420.21095
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029708
X-RAY DIFFRACTIONr_gen_planes_other00.021773
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A10588
12B10588
21A10568
22C10568
31B10604
32C10604
LS refinement shellResolution: 2.8→2.872 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.506 48 -
Rwork0.529 857 -
all-905 -
obs--34.63 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.97530.37951.57982.2330.96682.30350.0666-0.1029-0.53630.61060.2084-0.37480.32910.2252-0.2750.3358-0.00730.00040.1287-0.06430.225952.899525.644321.1993
21.8525-1.11620.50893.62660.34561.7428-0.0197-0.21310.23570.64520.1694-0.7354-0.37570.5536-0.14980.6381-0.2119-0.13160.3167-0.1080.193762.793159.033338.4284
31.01630.92860.43264.49931.82051.5318-0.09470.02060.1436-0.3408-0.18140.4708-0.7053-0.21270.27610.50190.0586-0.03030.0809-0.08160.120232.995358.079213.7424
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A46 - 424
2X-RAY DIFFRACTION2B46 - 424
3X-RAY DIFFRACTION3C46 - 424

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