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- PDB-9bu5: CC ProXp-ala apo solution structure -

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Basic information

Entry
Database: PDB / ID: 9bu5
TitleCC ProXp-ala apo solution structure
ComponentsDNA-binding protein, putative
KeywordsRNA BINDING PROTEIN
Function / homologyProlyl-tRNA editing protein ProX/PRXD1 / YbaK/aminoacyl-tRNA synthetase-associated domain / Aminoacyl-tRNA editing domain / YbaK/aminoacyl-tRNA synthetase-associated domain superfamily / aminoacyl-tRNA deacylase activity / DNA binding / DNA-binding protein, putative
Function and homology information
Biological speciesCaulobacter vibrioides (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsDuran, A.D. / Foster, M.P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM111135 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM141880 United States
Citation
Journal: Biomol.Nmr Assign. / Year: 2024
Title: NMR-based solution structure of the Caulobacter crescentus ProXp-ala trans-editing enzyme.
Authors: Duran, A.D. / Danhart, E.M. / Ma, X. / Nagy, A.B.K. / Musier-Forsyth, K. / Foster, M.P.
#1: Journal: Biomol NMR Assign / Year: 2024
Title: NMR-based solution structure of the Caulobacter crescentus ProXp-ala trans-editing enzyme.
Authors: Duran, A.D. / Danhart, E.M. / Ma, X. / Nagy, A.B.K. / Musier-Forsyth, K. / Foster, M.P.
History
DepositionMay 16, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 13, 2024Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA-binding protein, putative


Theoretical massNumber of molelcules
Total (without water)18,5701
Polymers18,5701
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 150structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein DNA-binding protein, putative


Mass: 18570.400 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter vibrioides (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ABV9
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic1HNCO
121isotropic1HNCA
131isotropic1HN(CO)CA
141isotropic1HN(CA)CB
151isotropic1CBCA(CO)NH
161isotropic2(H)CCH-TOCSY
171isotropic2CCCH-TOCSY
181isotropic215N-NOESY
191isotropic213C-NOESY

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Sample preparation

DetailsType: solution
Contents: 0.680 mM [U-13C; U-15N] ProXp-ala, 0.001 % w/v DSS, 50 mM sodium phosphate, 10 mM sodium chloride, 90% H2O/10% D2O
Details: U-15N,13C labeled sample 50 mM NaPi, 10 mM NaCl, pH 7.5
Label: ProXp-ala / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.680 mMProXp-ala[U-13C; U-15N]1
0.001 % w/vDSSnatural abundance1
50 mMsodium phosphatenatural abundance1
10 mMsodium chloridenatural abundance1
Sample conditionsIonic strength: 50 mM sodium phosphate, 10 mM sodium chloride Not defined
Label: 1 / pH: 7.5 / Pressure: 1 bar / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameDeveloperClassification
NMRViewJohnson, One Moon Scientificchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
NMRViewJohnson, One Moon Scientificpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 150 / Conformers submitted total number: 20

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