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- PDB-5tm0: Solution NMR structures of two alternative conformations of E. co... -

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Basic information

Entry
Database: PDB / ID: 5tm0
TitleSolution NMR structures of two alternative conformations of E. coli tryptophan repressor in dynamic equilibrium
ComponentsTrp operon repressor
KeywordsTRANSCRIPTION / Structural Genomics / PSI-Biology / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


sequence-specific DNA binding / nucleic acid binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / cytoplasm
Similarity search - Function
TrpR-like / Trp repressor, bacterial / Trp repressor / TrpR-like superfamily / Trp repressor protein / Trp repressor/replication initiator / Trp Operon Repressor; Chain A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Trp operon repressor
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsHarish, B. / Swapna, G.V.T. / Kornhaber, G.J. / Montelione, G.T. / Carey, J. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Proteins / Year: 2017
Title: Multiple helical conformations of the helix-turn-helix region revealed by NOE-restrained MD simulations of tryptophan aporepressor, TrpR.
Authors: Harish, B. / Swapna, G.V. / Kornhaber, G.J. / Montelione, G.T. / Carey, J.
History
DepositionOct 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Trp operon repressor
B: Trp operon repressor
C: Trp operon repressor
D: Trp operon repressor


Theoretical massNumber of molelcules
Total (without water)49,4814
Polymers49,4814
Non-polymers00
Water0
1
A: Trp operon repressor
B: Trp operon repressor


Theoretical massNumber of molelcules
Total (without water)24,7402
Polymers24,7402
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_5551
2
C: Trp operon repressor
D: Trp operon repressor


Theoretical massNumber of molelcules
Total (without water)24,7402
Polymers24,7402
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 15all calculated structures submitted
RepresentativeModel #1fewest violations
DetailsThe protein is a dimer and the coordinates provided are for two sets of dimers, each representing an alternative protein conformation. Each model has 4 chains A,B,C and D. Chains A and B form one dimer in WT conformation, chains C and D form a second dimer in the distorted conformation

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Components

#1: Protein
Trp operon repressor


Mass: 12370.131 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: trpR, Z5995, ECs5351 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A882

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC
131isotropic13D HNCO
141isotropic13D HNCA
151isotropic13D CBCA(CO)NH
1101isotropic13D (H)CCH-TOCSY
191isotropic13D 1H-13C NOESY aliphatic
181isotropic13D 1H-13C NOESY aromatic
171isotropic13D 1H-15N NOESY
161isotropic13D HN(CO)CA
1121isotropic13D HBHA(CO)NH
1111isotropic13D HN(CA)CB

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Sample preparation

DetailsType: solution
Contents: 0.5 mM [U-100% 13C; U-100% 15N] Tryptohan aporepressor, 10 mM Tris-HCl buffer pH 5.7, 100 mM NaCl, 5 mM DTT, 0.02 % sodium azide, 90% H2O/10% D2O
Details: 10 mM Tris-HCl buffer pH 5.7, 100 mM NaCl, 5 mM DTT and 0.02 % NaN3
Label: apoTrpR / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMTryptohan aporepressor[U-100% 13C; U-100% 15N]1
10 mMTris-HCl buffer pH 5.7natural abundance1
100 mMNaClnatural abundance1
5 mMDTTnatural abundance1
0.02 %sodium azidenatural abundance1
Sample conditionsIonic strength: 100 mM / Label: [U-100% 13C; U-100% 15N] / pH: 5.7 / Pressure: 1 atm / Temperature: 313 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz / Details: Equipped with a 5mm cryoprobe

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Processing

NMR software
NameVersionDeveloperClassification
AutoAssign2.1.1Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
TopSpin2.3Bruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3Goddardpeak picking
GROMACS4.6.5Berendsen H, van der Spoel D, van Drunen R.structure calculation
GROMACS4.6.5Berendsen H, van der Spoel D, van Drunen R.refinement
RefinementMethod: molecular dynamics / Software ordinal: 5
Details: The coordinates provided are for two sets of models, each representing an alternative protein conformation that differ particularly in the segment of the protein sequence corresponding to helix E.
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 15 / Conformers submitted total number: 15

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