Mass: 4306.846 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: NIRB SIGMA-54 BINDING SITE NON-TEMPLATE STRAND
#3: Protein
RNApolymerasesigmafactorRpoN
Mass: 7488.800 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: rpoN / Plasmid: PSKB3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) with Rosetta.pLysS / References: UniProt: O66858
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Experimental details
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Experiment
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Type
1
1
1
3D C13-seperated[F1], C12-filtered[F2] NOESY
2
2
2
3D C13-seperated NOESY
3
3
3
3D 15N-seperated NOESY
1
4
1
2D C12-filtered[F1,F2] NOESY
1
5
1
2D C12-filtered[F1] NOESY
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Sample preparation
Details
Solution-ID
Contents
Solvent system
1
1 mM Sigma-54-DNA (U-15N U-13C) complex; 250 mM NaCl; 10 mM deuterated-HEPES, pH 6.9; 1 mM EDTA; 100% D2O
100% D2O
2
1 mM Sigma-54-DNA (U-15N U-13C) complex; 250 mM NaCl; 10 mM HEPES, pH 6.9; 1 mM EDTA; 90% H2O; 10% D2O
90% H2O/10% D2O
3
1 mM Sigma-54-DNA (U-15N) complex; 250 mM NaCl; 10 mM HEPES, pH 6.9; 1 mM EDTA; 90% H2O; 10% D2O
90% H2O/10% D2O
Sample conditions
Conditions-ID
Ionic strength
pH
Pressure (kPa)
Temperature (K)
1
250mMNaCl
6.9
ambient
318K
2
250mMNaCl
6.9
ambient
303K
3
250mMNaCl
6.9
ambient
303K
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NMR measurement
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelength
Relative weight: 1
NMR spectrometer
Type
Manufacturer
Model
Field strength (MHz)
Spectrometer-ID
Bruker DMX
Bruker
DMX
600
1
Bruker AVANCE
Bruker
AVANCE
600
2
Bruker AVANCE
Bruker
AVANCE
800
3
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Processing
NMR software
Name
Version
Developer
Classification
NMRPipe
2.3
Delaglioetal. 1995
processing
NMRView
5.0.4
JohnsonandBlevins. 1994
dataanalysis
CYANA
2.1
Guntert. 2004
structuresolution
X-PLOR
2.14
Schwietersetal. 2003
refinement
Amber
7
Caseetal. 2002
refinement
Refinement
Method: simulated annealing / Software ordinal: 1 Details: The 20-structure ensemble refined with XPLOR-NIH (PDB ID: 2O8K) were then subjected to 20 ps of simulated annealing using the SANDER module of AMBER 7.0 with the 1994 force field (ff94) and ...Details: The 20-structure ensemble refined with XPLOR-NIH (PDB ID: 2O8K) were then subjected to 20 ps of simulated annealing using the SANDER module of AMBER 7.0 with the 1994 force field (ff94) and the generalized Born solvent model. First, 0.5 ps of energy minimization was performed. Then simulated annealing was run from 300K to 0K using NMR distant and dihedral restraints, as well as a distance dependent dielectric and a nonbonding cutoff of 15A.
NMR representative
Selection criteria: lowest energy
NMR ensemble
Conformer selection criteria: all calculated structures submitted Conformers calculated total number: 20 / Conformers submitted total number: 19
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