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- PDB-5yjs: Structure of vicilin from Capsicum annuum -

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Basic information

Entry
Database: PDB / ID: 5yjs
TitleStructure of vicilin from Capsicum annuum
Componentsvicilin-like antimicrobial peptides 2-2
KeywordsPLANT PROTEIN / Cupin / 7S Globulin / Copper site / Binding pocket
Function / homology
Function and homology information


nutrient reservoir activity
Similarity search - Function
Cupin / Cupin 1 / Cupin / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (I) ION / 2-HYDROXYBENZOIC ACID / Vicilin-like antimicrobial peptides 2-2
Similarity search - Component
Biological speciesCapsicum annuum (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsShikhi, M. / Nair, D.T. / Salunke, D.M.
Funding support India, 1items
OrganizationGrant numberCountry
India
CitationJournal: Biochem. J. / Year: 2018
Title: Structure-guided identification of function: role ofCapsicum annuumvicilin during oxidative stress.
Authors: Shikhi, M. / Nair, D.T. / Salunke, D.M.
History
DepositionOct 11, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _entity.formula_weight
Revision 1.2Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: vicilin-like antimicrobial peptides 2-2
B: vicilin-like antimicrobial peptides 2-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3699
Polymers85,7132
Non-polymers6567
Water5,837324
1
A: vicilin-like antimicrobial peptides 2-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3116
Polymers42,8571
Non-polymers4545
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area410 Å2
ΔGint-32 kcal/mol
Surface area18520 Å2
MethodPISA
2
B: vicilin-like antimicrobial peptides 2-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0583
Polymers42,8571
Non-polymers2022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-11 kcal/mol
Surface area18620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.030, 148.030, 148.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein vicilin-like antimicrobial peptides 2-2 / Bell pepper


Mass: 42856.719 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Capsicum annuum (plant) / References: UniProt: A0A452CSM5*PLUS

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Non-polymers , 6 types, 331 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-SAL / 2-HYDROXYBENZOIC ACID / SALICYLIC ACID


Mass: 138.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O3
#5: Chemical ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsThe protein used in this structure was directly purified from its source. The sequence of this ...The protein used in this structure was directly purified from its source. The sequence of this protein was determined based on the high resolution crystal structure electron density map. The electron density corresponding to the UNK region was not clear most likely due to structural disorder and thus the sequence could not be determined.

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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: 2.88 Å3/Da / Density % sol: 57.26 % / Description: Cuboid shape
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 50mM HEPES, 12% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.16→50 Å / Num. obs: 55184 / % possible obs: 100 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.5
Reflection shellResolution: 2.16→2.28 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.622 / Mean I/σ(I) obs: 2.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.12phasing
Coot0.8.5model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CAD

5cad


Resolution: 2.16→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.505 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21671 2983 5.2 %RANDOM
Rwork0.17515 ---
obs0.17735 54852 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.354 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.16→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5808 0 37 324 6169
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0195968
X-RAY DIFFRACTIONr_bond_other_d0.0020.025673
X-RAY DIFFRACTIONr_angle_refined_deg1.8051.9558039
X-RAY DIFFRACTIONr_angle_other_deg1.02313013
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7435736
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.55124.054296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.66915994
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.311540
X-RAY DIFFRACTIONr_chiral_restr0.1140.2840
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216900
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021472
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9873.4292956
X-RAY DIFFRACTIONr_mcbond_other2.9873.4282955
X-RAY DIFFRACTIONr_mcangle_it4.1555.1193688
X-RAY DIFFRACTIONr_mcangle_other4.1545.123689
X-RAY DIFFRACTIONr_scbond_it4.2173.9023012
X-RAY DIFFRACTIONr_scbond_other4.2123.9023012
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.4735.6384352
X-RAY DIFFRACTIONr_long_range_B_refined8.16239.2786348
X-RAY DIFFRACTIONr_long_range_B_other8.16439.136297
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.162→2.218 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 222 -
Rwork0.265 3999 -
obs--100 %

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