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Yorodumi- PDB-5tm0: Solution NMR structures of two alternative conformations of E. co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5tm0 | ||||||
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Title | Solution NMR structures of two alternative conformations of E. coli tryptophan repressor in dynamic equilibrium | ||||||
Components | Trp operon repressor | ||||||
Keywords | TRANSCRIPTION / 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 | ||||||
Biological species | Escherichia coli O157:H7 (bacteria) | ||||||
Method | SOLUTION NMR / molecular dynamics | ||||||
Authors | Harish, B. / Swapna, G.V.T. / Kornhaber, G.J. / Montelione, G.T. / Carey, J. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5tm0.cif.gz | 2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5tm0.ent.gz | 1.7 MB | Display | PDB format |
PDBx/mmJSON format | 5tm0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5tm0_validation.pdf.gz | 504.6 KB | Display | wwPDB validaton report |
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Full document | 5tm0_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 5tm0_validation.xml.gz | 252.5 KB | Display | |
Data in CIF | 5tm0_validation.cif.gz | 239.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tm/5tm0 ftp://data.pdbj.org/pub/pdb/validation_reports/tm/5tm0 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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NMR ensembles |
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Details | The 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 |
-Components
#1: Protein | 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
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: 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 | ||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 100 mM / Label: [U-100% 13C; U-100% 15N] / pH: 5.7 / Pressure: 1 atm / Temperature: 313 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz / Details: Equipped with a 5mm cryoprobe |
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-Processing
NMR software |
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Refinement | Method: 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 representative | Selection criteria: fewest violations | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: all calculated structures submitted Conformers calculated total number: 15 / Conformers submitted total number: 15 |