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- PDB-2hfv: Solution NMR Structure of Protein RPA1041 from Pseudomonas aerugi... -

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Basic information

Entry
Database: PDB / ID: 2hfv
TitleSolution NMR Structure of Protein RPA1041 from Pseudomonas aeruginosa. Northeast Structural Genomics Consortium Target PaT90.
ComponentsHypothetical Protein RPA1041Hypothesis
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / NESG / GFT-NMR / alpha+beta / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


urea metabolic process / nickel cation binding / protein-containing complex assembly
Similarity search - Function
Domain of unknown function DUF2007 / : / Putative prokaryotic signal transducing protein / UreE, C-terminal domain / Nitrogen regulatory PII-like, alpha/beta / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DUF2007 domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodSOLUTION NMR / Refinement in explicit water bath
AuthorsEletsky, A. / Atreya, H.S. / Liu, G. / Sukumaran, D. / Garcia, M. / Yee, A. / Arrowsmith, C. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: TO BE PUBLISHED
Title: Solution NMR Structure of Pseudomonas aeruginosa Hypothetical Protein RPA1041
Authors: Eletsky, A. / Atreya, H.S. / Liu, G. / Sukumaran, D. / Garcia, M. / Yee, A. / Arrowsmith, C. / Szyperski, T.
History
DepositionJun 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 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_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999SEQUENCE AT THE TIME OF PROCESSING, THE SEQUENCE OF THIS PROTEIN IS NOT AVAILABLE AT THE UNP ...SEQUENCE AT THE TIME OF PROCESSING, THE SEQUENCE OF THIS PROTEIN IS NOT AVAILABLE AT THE UNP SEQUENCE DATABASE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical Protein RPA1041


Theoretical massNumber of molelcules
Total (without water)10,6161
Polymers10,6161
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 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Hypothetical Protein RPA1041 / Hypothesis


Mass: 10615.876 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 gold magic / References: UniProt: Q6NAY9

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N,13C-separated NOESY
121(4,3)D GFT HNNCABCA
131(4,3)D GFT CABCA(CO)NHN
1413D HAB(CO)NH
151(4,3)D GFT (H)CCH-COSYali
1613D (H)CCH-TOCSYali

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Sample preparation

DetailsContents: 10 mM MOPS, 450 mM NaCl, ~10 uM ZnSO4, 10 mM DTT, 0.01% NaN3, 1mM benzamidine, 1x inhibitor cocktail, 90% H2O / 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 450 mM / pH: 6.5 / Pressure: 1 atm / Temperature: 298 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 INOVAVarianINOVA6001
Varian INOVAVarianINOVA7502

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVarian, Inc.collection
XEASY1.3.13Bartels, Ch.data analysis
CARA1.5.3Keller, R.data analysis
CYANA2.1Guentert, P.structure solution
CNS1.1BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ,RICE,SIMONSON,WARRENrefinement
AutoStructure2.0.0Huang, Y. J.structure solution
PROSA6Guentert, P.processing
RefinementMethod: Refinement in explicit water bath / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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