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- PDB-9cch: Solution structure of the Bsu Anti-TRAP trimer -

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Basic information

Entry
Database: PDB / ID: 9cch
TitleSolution structure of the Bsu Anti-TRAP trimer
ComponentsAnti-TRAP regulator
KeywordsGENE REGULATION / inhibitor / zinc ribbon / trp operon
Function / homologyTryptophan RNA-binding attenuator protein inhibitory protein / Tryptophan RNA-binding attenuator protein inhibitory protein / Heat shock protein DnaJ, cysteine-rich domain superfamily / Anti-TRAP regulator
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / SOLUTION SCATTERING / simulated annealing
AuthorsFoster, M.P. / McElroy, C.A. / Ihms, E.C. / Kumar Yadav, D.
Funding support United States, 9items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM077234 United States
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)S10 OD018483 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM124168 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM141955 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM008512 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41 GM128577 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM120923 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM062750 United States
CitationJournal: To Be Published
Title: Solution structure of the Bsu Anti-TRAP trimer
Authors: Foster, M.P. / McElroy, C.A. / Ihms, E.C. / Kumar Yadav, D.
History
DepositionJun 21, 2024Deposition site: RCSB / Processing site: RCSB
SupersessionJun 25, 2025ID: 2KO8
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Anti-TRAP regulator
B: Anti-TRAP regulator
C: Anti-TRAP regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2476
Polymers17,0513
Non-polymers1963
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, not applicable, NMR Distance Restraints, NMR relaxation study, mass spectrometry, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Anti-TRAP regulator


Mass: 5683.575 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: rtpA, J5227_14785 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A063XE83
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

Experiment
Method
SOLUTION NMR
SOLUTION SCATTERING
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic12D 1H-13C HSQC
121isotropic12D 1H-15N HSQC
131isotropic12D 1H-15N TROSY-HSQC
142isotropic13D 1H-13C NOESY
151isotropic13D 1H-15N NOESY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution12 mM [U-15N] f AT, 20 mM [U-100% 2H] TRIS, 20 mM beta-mercaptoethanol, 1 mM zinc chloride, 90% H2O/10% D2OpH was measured at 298 K; experiments performed at 328 K (55 C). Protein concentration is monomer concentration15N_sample90% H2O/10% D2O
solution28 mM [U-15N] f AT, 20 mM [U-100% 2H] TRIS, 20 mM beta-mercaptoethanol, 1 mM zinc chloride, 90% H2O/10% D2OpH was measured at 298 K; experiments performed at 328 K (55 C). Protein concentration is monomer concentration15N13C_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMf AT[U-15N]1
20 mMTRIS[U-100% 2H]1
20 mMbeta-mercaptoethanolnatural abundance1
1 mMzinc chloridenatural abundance1
8 mMf AT[U-15N]2
20 mMTRIS[U-100% 2H]2
20 mMbeta-mercaptoethanolnatural abundance2
1 mMzinc chloridenatural abundance2
Sample conditionsDetails: 20 mM [U-2H] TRIS, 20 mM beta-mercaptoethanol, 1 mM ZnCl2
Ionic strength: 20 mM / Label: NMR buffer / pH: 7.5 pH* / Pressure: 1 atm / Temperature: 328 K

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Data collection

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker DRXBrukerDRX8001
Bruker DRXBrukerDRX6002
Bruker AVANCEBrukerAVANCE8003updated console
Bruker AVANCEBrukerAVANCE6004updated console

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Processing

NMR software
NameDeveloperClassification
NMRViewJBruce Johnsonchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure 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: 100 / Conformers submitted total number: 20

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