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- PDB-1vfi: Solution Structure of Vanabin2 (RUH-017), a Vanadium-binding Prot... -

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Basic information

Entry
Database: PDB / ID: 1vfi
TitleSolution Structure of Vanabin2 (RUH-017), a Vanadium-binding Protein from Ascidia sydneiensis samea
Componentsvanadium-binding protein 2
KeywordsMETAL BINDING PROTEIN / vanadium-binding / Ascidian / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases) / oxidoreductase activity / metal ion binding / cytoplasm
Similarity search - Function
Vanadium-binding protein 2 / Vanadium-binding protein 2 / Vanadium-binding protein 2 superfamily / Vanadium-binding protein 2 / Serum Albumin; Chain A, Domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Vanadium-binding protein 2
Similarity search - Component
Biological speciesAscidia sydneiensis samea (invertebrata)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsHamada, T. / Hirota, H. / Asanuma, M. / Hayashi, F. / Kobayashi, N. / Ueki, T. / Michibata, H. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Am.Chem.Soc. / Year: 2005
Title: Solution Structure of Vanabin2, a Vanadium(IV)-Binding Protein from the Vanadium-Rich Ascidian Ascidia sydneiensis samea
Authors: Hamada, T. / Asanuma, M. / Ueki, T. / Hayashi, F. / Kobayashi, N. / Yokoyama, S. / Michibata, H. / Hirota, H.
History
DepositionApr 13, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: vanadium-binding protein 2


Theoretical massNumber of molelcules
Total (without water)10,5071
Polymers10,5071
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations, structures with the lowest energy, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein vanadium-binding protein 2 / Vanabin2 / RUH-017


Mass: 10507.256 Da / Num. of mol.: 1 / Fragment: residues 1-95
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ascidia sydneiensis samea (invertebrata)
Species: Ascidia sydneiensis / Strain: samea / Plasmid: pMAL-c / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q86BW2
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
NMR detailsText: This structure was determined using 3D NMR techniques

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Sample preparation

DetailsContents: 0.7mM vanadium-binding protein U-15N, 13C; 20mM potassium phosphate buffer (pH 6.9)
Solvent system: 90% H2O/10% D2O
Sample conditionspH: 7 / Pressure: ambient / Temperature: 303 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe21_2Delaglio, F.collection
NMRView5.0.4Johnson, B. A.data analysis
KUJIRA0.8995Kobayashi, N.structure solution
CYANA1.0.7Guentert, P.structure solution
CYANA1.0.7Guentert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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