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- PDB-1vee: NMR structure of the hypothetical rhodanese domain At4g01050 from... -

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Basic information

Entry
Database: PDB / ID: 1vee
TitleNMR structure of the hypothetical rhodanese domain At4g01050 from Arabidopsis thaliana
Componentsproline-rich protein family
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / hypothetical protein / rhodanese domain / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


chloroplast thylakoid membrane protein complex / chloroplast thylakoid / chloroplast envelope / photosynthetic electron transport in photosystem II / chloroplast thylakoid membrane / chloroplast / cytosol
Similarity search - Function
Rhodanese-like domain-containing protein STR4-like / Rhodanese-like domain / Oxidized Rhodanese; domain 1 / Rhodanese-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Rhodanese-like domain-containing protein 4, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsPantoja-Uceda, D. / Lopez-Mendez, B. / Koshiba, S. / Inoue, M. / Kigawa, T. / Terada, T. / Shirouzu, M. / Tanaka, A. / Seki, M. / Shinozaki, K. ...Pantoja-Uceda, D. / Lopez-Mendez, B. / Koshiba, S. / Inoue, M. / Kigawa, T. / Terada, T. / Shirouzu, M. / Tanaka, A. / Seki, M. / Shinozaki, K. / Yokoyama, S. / Guntert, P. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Citation
Journal: Protein Sci. / Year: 2005
Title: Solution structure of the rhodanese homology domain At4g01050(175-295) from Arabidopsis thaliana
Authors: Pantoja-Uceda, D. / Lopez-Mendez, B. / Koshiba, S. / Inoue, M. / Kigawa, T. / Terada, T. / Shirouzu, M. / Tanaka, A. / Seki, M. / Shinozaki, K. / Yokoyama, S. / Guntert, P.
#1: Journal: J.Biomol.NMR / Year: 2004
Title: NMR Assignment of the Hypothetical Rhodanese Domain At4g01050 from Arabidopsis Thaliana
Authors: Pantoja-Uceda, D. / Lopez-Mendez, B. / Koshiba, S. / Kigawa, T. / Shirouzu, M. / Terada, T. / Inoue, M. / Yabuki, T. / Aoki, M. / Seki, E. / Matsuda, T. / Hirota, H. / Yoshida, M. / Tanaka, ...Authors: Pantoja-Uceda, D. / Lopez-Mendez, B. / Koshiba, S. / Kigawa, T. / Shirouzu, M. / Terada, T. / Inoue, M. / Yabuki, T. / Aoki, M. / Seki, E. / Matsuda, T. / Hirota, H. / Yoshida, M. / Tanaka, A. / Osanai, T. / Seki, M. / Shinozaki, K. / Yokoyama, S. / Guntert, P.
History
DepositionMar 30, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 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_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: proline-rich protein family


Theoretical massNumber of molelcules
Total (without water)14,2021
Polymers14,2021
Non-polymers00
Water0
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
RepresentativeModel #1closest to the average

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Components

#1: Protein proline-rich protein family / hypothetical protein RAFL06-68-J04


Mass: 14201.863 Da / Num. of mol.: 1 / Fragment: RHODANESE HYPOTHETICAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Description: E.COLI CELL-FREE PROTEIN SYNTHESIS / Gene: RIKEN CDNA RAFL06-68-J04 / Plasmid: P030120-27 / References: UniProt: Q9M158

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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

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Sample preparation

DetailsContents: 1.1mM 13C, 15N-arabidopsis rhodanese hypothetical domain; 20mM Phosphate buffer; 100mM NA 1mM dithiothreitol; 0.02% NA3N; 90% H2O, 10% D2O
Sample conditionsIonic strength: NULL / pH: 7.0 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
OPALp1.3R.KORADI,M.BILLETER,P.GUNTERTrefinement
CYANA2.0.29P.GUNTERT ET AL.structure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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