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- PDB-1nwb: Solution NMR Structure of Protein AQ_1857 from Aquifex aeolicus: ... -

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Basic information

Entry
Database: PDB / ID: 1nwb
TitleSolution NMR Structure of Protein AQ_1857 from Aquifex aeolicus: Northeast Structural Genomics Consortium Target QR6.
ComponentsHypothetical protein AQ_1857
Keywordsstructural genomics / unknown function / QR6 / protein structure initiative / NESG / Reduced Dimensionality NMR / PSI / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


protein maturation by iron-sulfur cluster transfer / iron-sulfur cluster assembly / 2 iron, 2 sulfur cluster binding / structural molecule activity / cytoplasm
Similarity search - Function
FeS cluster insertion, C-terminal, conserved site / Hypothetical hesB/yadR/yfhF family signature. / FeS cluster insertion protein / Hypothetical Protein Aq_1857; Chain: A; / HesB-like domain / FeS cluster biogenesis / HesB-like domain superfamily / Iron-sulphur cluster biosynthesis / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesAquifex aeolicus (bacteria)
MethodSOLUTION NMR / distance geometry torsion angle dynamics
AuthorsXu, D. / Liu, G. / Xiao, R. / Acton, T. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Proteins / Year: 2004
Title: NMR structure of the hypothetical protein AQ-1857 encoded by the Y157 gene from Aquifex aeolicus reveals a novel protein fold.
Authors: Xu, D. / Liu, G. / Xiao, R. / Acton, T. / Goldsmith-Fischman, S. / Honig, B. / Montelione, G.T. / Szyperski, T.
History
DepositionFeb 5, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 22, 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: Hypothetical protein AQ_1857


Theoretical massNumber of molelcules
Total (without water)13,7401
Polymers13,7401
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 #1fewest violations

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Components

#1: Protein Hypothetical protein AQ_1857


Mass: 13740.300 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: AQ_1857 / Plasmid: pET21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O67709

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
131HNHA
242ct-13C-HSQC
1513D-HNNCACB
1613D-RD-HABCAB(CO)NHN
1713D-RD-(H)CCH-COSY
NMR detailsText: This structure was determined with the help of Reduced Dimensionality NMR Spectroscopy

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Sample preparation

Details
Solution-IDContentsSolvent system
11.08mM QR6 U-15N,13C20mM MES, 50mM NaCl, 5mM DTT, 5% D2O, 0.02% NaN3
21.01mM QR6 100% 15N, 5%13C20mM MES, 100mM NaCl, 5mM CaCl2, 10mM DTT, 5% D2O, 0.02% NaN3
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
16.5 ambient 293 K
26.5 ambient 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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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 INOVAVarianINOVA6001
Varian INOVAVarianINOVA7502

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guentertstructure solution
NMRPipe1Baxprocessing
XEASY1.3.1Tai-he Xiadata analysis
PROSA5Guentertprocessing
CYANA1.0.3Guentertstructure solution
CYANA1.0.3Guentertrefinement
RefinementMethod: distance geometry torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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