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- PDB-2dcq: Fully automated NMR structure determination of the rhodanese homo... -

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Basic information

Entry
Database: PDB / ID: 2dcq
TitleFully automated NMR structure determination of the rhodanese homology domain At4g01050(175-295) from Arabidopsis thaliana
ComponentsPutative protein At4g01050
KeywordsUNKNOWN FUNCTION / rhodanese domain / fully automated structure determination / FLYA algorithm
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 / Fully automated NMR spectrum analysis, structure calculation without human intervention. CHEMICAL SHIFT ASSIGNMENTS, CONFORMATIONAL RESTRAINTS HAVE NOT BEEN VERIFIED MANUALLY.
AuthorsLopez-Mendez, B. / Guntert, P.
Citation
Journal: J.AM.CHEM.SOC. / Year: 2006
Title: Automated protein structure determination from NMR spectra
Authors: Lopez-Mendez, B. / Guntert, P.
#1: 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.
#2: 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
DepositionJan 12, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 17, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / 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_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: 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: Putative protein At4g01050


Theoretical massNumber of molelcules
Total (without water)14,2021
Polymers14,2021
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
RepresentativeModel #1

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Components

#1: Protein Putative protein At4g01050 / 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 / Production host: Cell free synthesis / 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
Solvent system: 90% H2O/10% D2O
Sample conditionspH: 7 / 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
FLYA1Lopez-Mendez, B,, Guntert, P.structure solution
CYANA2.1Guntert, P. et al.structure solution
OPALp1.2Koradi, R., Billeter, M., Guntert, P.refinement
RefinementMethod: Fully automated NMR spectrum analysis, structure calculation without human intervention. CHEMICAL SHIFT ASSIGNMENTS, CONFORMATIONAL RESTRAINTS HAVE NOT BEEN VERIFIED MANUALLY.
Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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