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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 / defense response to bacterium / integral component of membrane / cytosol
Rhodanese-like domain superfamily
Rhodanese-like domain-containing protein 4, chloroplastic
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. / 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, A. / Osanai, T. / Seki, M. / Shinozaki, K. / Yokoyama, S. / Guntert, P.
Validation Report
SummaryFull reportAbout validation report
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

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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
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/peptide 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-ID: 1 / Solution-ID: 1

Experiment-IDType
13D 15N-SEPARATED NOESY
23D 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

Manufacturer: Bruker

TypeModelField strength (MHz)Spectrometer-ID
Bruker DRXDRX6001
Bruker AvanceAvance8002

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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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