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- PDB-6v7j: The C2221 crystal form of canavalin at 173 K -

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Basic information

Entry
Database: PDB / ID: 6v7j
TitleThe C2221 crystal form of canavalin at 173 K
ComponentsCanavalin
KeywordsPLANT PROTEIN / storage protein / trimer / benzoic acid / enzyme
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 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)152,05712
Polymers151,2943
Non-polymers7639
Water8,593477
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18000 Å2
ΔGint-121 kcal/mol
Surface area37940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.347, 149.247, 128.046
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 0 / 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: 50431.469 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 / Benzoic acid


Mass: 122.121 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 477 / 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: 2.33 Å3/Da / Density % sol: 47 %
Description: Rectangular blocks with edge lengths that occasionally exceeded 1.5 mm
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Vapor diffusion in Cryschem sitting drop plates at room temperature. Reservoirs were Dulbeccos Phosphate buffered saline at pH 6.5. Drops were equal amounts of the reservoir and a 40 mg/ml ...Details: Vapor diffusion in Cryschem sitting drop plates at room temperature. Reservoirs were Dulbeccos Phosphate buffered saline at pH 6.5. Drops were equal amounts of the reservoir and a 40 mg/ml solution of the protein dissolved in water with a trace of ammonium hydroxide. Crystallization time was 24 to 48 hours.
PH range: 6.0 - 6.8

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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→50.01 Å / Num. obs: 72246 / % possible obs: 82 % / Redundancy: 9.2 % / Biso Wilson estimate: 56 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.052 / Rrim(I) all: 0.176 / Rsym value: 0.16 / Net I/σ(I): 5.8
Reflection shellResolution: 2→2.03 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 0.6 / Num. unique obs: 2336 / CC1/2: 0.133 / % possible all: 43.4

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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→50.01 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 15.997 / SU ML: 0.194 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.23 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2474 3636 5.1 %RANDOM
Rwork0.1957 ---
obs0.1982 67935 81.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 146.89 Å2 / Biso mean: 47.735 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--1.63 Å20 Å20 Å2
2---1.83 Å20 Å2
3---3.46 Å2
Refinement stepCycle: final / Resolution: 2→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8496 0 48 478 9022
Biso mean--62.41 53.11 -
Num. residues----1055
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0138812
X-RAY DIFFRACTIONr_bond_other_d00.0178121
X-RAY DIFFRACTIONr_angle_refined_deg1.3451.64711952
X-RAY DIFFRACTIONr_angle_other_deg1.2091.57318929
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.14751083
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.92523.008532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.666151559
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6931566
X-RAY DIFFRACTIONr_chiral_restr0.0560.21115
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029899
X-RAY DIFFRACTIONr_gen_planes_other00.021807
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A10780
12B10780
21A10672
22C10672
31B10742
32C10742
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 148 -
Rwork0.395 2752 -
all-2900 -
obs--44.91 %
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)
10.0494-0.0861-0.07180.4996-0.22160.71060.02180.016-0.0708-0.0323-0.03780.0825-0.01950.00150.0160.22060.008-0.03220.0193-0.02660.169451.927216.13913.6705
20.0851-0.1784-0.14380.64480.1080.55930.01780.01250.02330.0220.02740.0395-0.0650.007-0.04530.2650.0310.00930.04510.01420.131149.458554.308910.6998
30.0534-0.1401-0.08810.9371-0.07240.361-0.0143-0.0023-0.01260.1040.045-0.0061-0.0691-0.0283-0.03080.24590.0278-0.00220.0138-0.00230.140146.114437.140245.0249
40000000000000000.1083000.108300.1083000
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A46 - 424
2X-RAY DIFFRACTION2B46 - 424
3X-RAY DIFFRACTION3C46 - 424
4X-RAY DIFFRACTION4C0

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