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- PDB-2ko8: The Structure of Anti-TRAP -

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Basic information

Entry
Database: PDB / ID: 2ko8
TitleThe Structure of Anti-TRAP
ComponentsTryptophan RNA-binding attenuator protein inhibitory protein
KeywordsTRANSCRIPTION REGULATOR / Protein / Transcription / Transcription regulation
Function / homology
Function and homology information


identical protein binding / cytoplasm
Similarity search - Function
Chaperone, DNAj Protein; Chain A / Chaperone, DNAj Protein; Chain A - #10 / Tryptophan RNA-binding attenuator protein inhibitory protein / Tryptophan RNA-binding attenuator protein inhibitory protein / Heat shock protein DnaJ, cysteine-rich domain superfamily / Other non-globular / Special
Similarity search - Domain/homology
Tryptophan RNA-binding attenuator protein inhibitory protein
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsMcElroy, C.A. / Gollnick, P. / Foster, M.P.
CitationJournal: To be Published
Title: Solution Structure of the B. subtilis Anti-TRAP trimer and its Interaction with TRAP
Authors: McElroy, C.A. / Gollnick, P. / Foster, M.P.
History
DepositionSep 12, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Database references / Derived calculations / Other / Category: database_2 / pdbx_database_status / struct_conn
Item: _pdbx_database_status.status_code_cs / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tryptophan RNA-binding attenuator protein inhibitory protein
B: Tryptophan RNA-binding attenuator protein inhibitory protein
C: Tryptophan RNA-binding attenuator protein inhibitory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2476
Polymers17,0513
Non-polymers1963
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 / 300structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Tryptophan RNA-binding attenuator protein inhibitory protein / Anti-TRAP protein / AT


Mass: 5683.575 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: BSU02530, rtpA, yczA / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: UniProt: O31466
#2: Chemical ChemComp-ZN / ZINC ION


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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D HN(CA)CB
1413D C(CO)NH
1513D H(CCO)NH
1623D (H)CCH-COSY
1713D 1H-15N TOCSY
1822D 1H-13C HSQC
1913D HNHA
11013D HNHB
11113D HACAHB-COSY
11223D 1H-13C NOESY
11313D 1H-15N/13C TIME-SHARED NOESY
11422D (H)CCH-COSY AROMATIC
11522D 1H-13C HSQC aromatic
11612D IPAP
11712D 15N HETERONUCLEAR NOE
11812D 15N HETERONUCLEAR T2
11912D 15N HETERONUCLEAR T1

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Sample preparation

Details
Solution-IDContentsSolvent system
15-10 mM [U-13C; U-15N] protein, 20 mM [U-2H] TRIS, 20 mM beta-mercaptoethanol, 1 mM ZnCl2, 90% H2O/10% D2O90% H2O/10% D2O
25-10 mM [U-13C; U-15N] protein, 20 mM [U-2H] TRIS, 20 mM beta-mercaptoethanol, 1 mM ZnCl2, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMentity_1-1[U-13C; U-15N]5-101
20 mMTRIS-2[U-2H]1
20 mMbeta-mercaptoethanol-31
1 mMZnCl2-41
mMentity_1-5[U-13C; U-15N]5-102
20 mMTRIS-6[U-2H]2
20 mMbeta-mercaptoethanol-72
1 mMZnCl2-82
Sample conditionsIonic strength: 20 / pH: 7.5 / Pressure: ambient / Temperature: 328 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificdata analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
ARIALinge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Last round of refinement was performed in ARIA and included explicit solvent
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 300 / Conformers submitted total number: 20

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