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- PDB-5cad: Crystal structure of the vicilin from Solanum melongena revealed ... -

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Basic information

Entry
Database: PDB / ID: 5cad
TitleCrystal structure of the vicilin from Solanum melongena revealed existence of different anionic ligands in structurally similar pockets
ComponentsSM80.1 Vicilin
KeywordsPLANT PROTEIN / Solanaceae / Solanum melongena / 7S vicilin / SM80.1
Function / homology
Function and homology information


: / 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
ACETATE ION / PYROGLUTAMIC ACID / SM80.1 Vicilin
Similarity search - Component
Biological speciesSolanum melongena (eggplant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.49 Å
AuthorsJain, A. / Kumar, A. / Salunke, D.M.
CitationJournal: Sci Rep / Year: 2016
Title: Crystal structure of the vicilin from Solanum melongena reveals existence of different anionic ligands in structurally similar pockets
Authors: Jain, A. / Kumar, A. / Salunke, D.M.
History
DepositionJun 29, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SM80.1 Vicilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8564
Polymers42,6441
Non-polymers2123
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-6 kcal/mol
Surface area17990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.330, 119.330, 158.190
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein SM80.1 Vicilin


Mass: 42643.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum melongena (eggplant) / Tissue: seed / References: UniProt: A0A158RFR1*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-PCA / PYROGLUTAMIC ACID


Type: L-peptide linking / Mass: 129.114 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H7NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.33 % / Description: Hexagonal crystal
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 50mM Tris-Cl, 1.5 M Sodium malonate, 10% Peg 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.49→22.71 Å / Num. obs: 70495 / % possible obs: 99.9 % / Redundancy: 11.8 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 20.5
Reflection shellResolution: 1.49→1.57 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 4.3 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.3refinement
PDB_EXTRACT3.15data extraction
PHENIX1.8.1phasing
Coot0.6model building
iMOSFLMdata processing
MxCuBEdata collection
RefinementMethod to determine structure: SAD / Resolution: 1.49→22.71 Å / Cross valid method: FREE R-VALUE / σ(F): 23
RfactorNum. reflection% reflectionSelection details
Rfree0.2102 3556 5 %Random selection
Rwork0.1994 66896 --
obs-70452 99.9 %-
Solvent computationBsol: 59.2503 Å2
Displacement parametersBiso max: 67.63 Å2 / Biso mean: 21.2462 Å2 / Biso min: 1.05 Å2
Baniso -1Baniso -2Baniso -3
1--3.122 Å20 Å20 Å2
2---3.122 Å20 Å2
3---6.243 Å2
Refinement stepCycle: final / Resolution: 1.49→22.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2912 0 14 256 3182
Biso mean--32.31 30.46 -
Num. residues----379
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_d1.969
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param
X-RAY DIFFRACTION5CNS_TOPPAR:carbohydrate.param
X-RAY DIFFRACTION6cnsACT.param
X-RAY DIFFRACTION7cnsPCA.param

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