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- PDB-5vf5: Crystal structure of the vicilin from Solanum melongena, re-refinement -

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Basic information

Entry
Database: PDB / ID: 5vf5
TitleCrystal structure of the vicilin from Solanum melongena, re-refinement
ComponentsSM80.1 Vicilin
KeywordsPLANT PROTEIN / 7S VICILIN SM80.1 PLANT PROTEIN SEQUENCE ASSIGNMENT RE-REFINEMENT
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 / COPPER (II) ION / MALONATE ION / DI(HYDROXYETHYL)ETHER / SM80.1 Vicilin
Similarity search - Component
Biological speciesSolanum melongena (eggplant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.49 Å
AuthorsPorebski, P.J. / Wlodawer, A. / Dauter, Z. / Minor, W. / Stanfield, R. / Jaskolski, M. / Pozharski, E. / Weichenberger, C.X. / Rupp, B.
Funding support United States, Austria, Poland, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U01HG008424, R01GM117080, R01GM117325 United States
Austrian Science FundP28395-B26 Austria
Polish National Science Centre2013/10/M/NZ1/00251 Poland
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
DepositionApr 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 1.4Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 0THIS ENTRY 5VF5 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 5CAD, DETERMINED BY A. ...THIS ENTRY 5VF5 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 5CAD, DETERMINED BY A.JAIN,A.KUMAR,D.M.SALUNKE

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SM80.1 Vicilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1156
Polymers48,7611
Non-polymers3545
Water6,341352
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-15 kcal/mol
Surface area18290 Å2
2
A: SM80.1 Vicilin
hetero molecules

A: SM80.1 Vicilin
hetero molecules

A: SM80.1 Vicilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,34518
Polymers146,2843
Non-polymers1,06115
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area18850 Å2
ΔGint-107 kcal/mol
Surface area38480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.330, 119.330, 158.190
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-666-

HOH

21A-915-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein SM80.1 Vicilin


Mass: 48761.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum melongena (eggplant) / Tissue: SEED / References: UniProt: A0A2R2JFS1*PLUS

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Non-polymers , 6 types, 357 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.56 Å3/Da / Density % sol: 51.97 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 5CAD
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 50mM Tris-Cl, 1.5 M Sodium malonate, 10% Peg 3350 / PH range: 8

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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

SoftwareName: REFMAC / Version: 5.8.0158 / Classification: refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5CAD

5cad


Resolution: 1.49→22.71 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.969 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.057 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16263 3556 5 %RANDOM
Rwork0.13052 ---
obs0.13215 66897 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.839 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å2-0.27 Å20 Å2
2---0.55 Å20 Å2
3---1.77 Å2
Refinement stepCycle: LAST / Resolution: 1.49→22.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2948 0 20 352 3320
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193371
X-RAY DIFFRACTIONr_bond_other_d0.0030.023088
X-RAY DIFFRACTIONr_angle_refined_deg1.6861.9414585
X-RAY DIFFRACTIONr_angle_other_deg1.5237176
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4025443
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.3823.125192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.8315591
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5661539
X-RAY DIFFRACTIONr_chiral_restr0.1210.2478
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023896
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02787
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_it2.1331.7451597
X-RAY DIFFRACTIONr_mcbond_other2.1235.0791595
X-RAY DIFFRACTIONr_mcangle_it2.4512010
X-RAY DIFFRACTIONr_mcangle_other2.452011
X-RAY DIFFRACTIONr_scbond_it3.5361774
X-RAY DIFFRACTIONr_scbond_other3.5381772
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0382543
X-RAY DIFFRACTIONr_long_range_B_refined4.2233638
X-RAY DIFFRACTIONr_long_range_B_other4.2223639
X-RAY DIFFRACTIONr_rigid_bond_restr5.06333336
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded11.25623235
LS refinement shellResolution: 1.49→1.529 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.207 270 -
Rwork0.171 4888 -
obs--99.83 %

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