Mass: 13248.225 Da / Num. of mol.: 1 / Fragment: UNP residues 25-135 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 / Gene: sap1, SPCC1672.02c / Production host: Escherichia coli (E. coli) / References: UniProt: P40847
#2: DNA chain
DNA (5'-D(*CP*AP*AP*AP*AP*CP*AP*AP*TP*AP*TP*T)-3')
Mass: 3638.432 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Schizosaccharomyces pombe (fission yeast)
#3: DNA chain
DNA (5'-D(*AP*AP*TP*AP*TP*TP*GP*TP*TP*TP*TP*G)-3')
Mass: 3682.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Schizosaccharomyces pombe (fission yeast)
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Experimental details
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Experiment
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Sample state
Spectrometer-ID
Type
1
1
1
isotropic
1
2D 1H-15N HSQC
1
7
1
isotropic
1
3DCBCA(CO)NH
1
8
1
isotropic
1
3D HN(CA)CB
1
12
1
isotropic
1
3D HNCO
1
9
2
isotropic
1
2D 1H-15N HSQC
1
5
2
isotropic
1
3DCBCA(CO)NH
1
6
2
isotropic
1
3D HN(CA)CB
1
10
2
isotropic
1
3D HNCO
1
11
2
isotropic
1
3D HNCA
1
2
2
isotropic
3
3D 1H-15N NOESY
1
3
2
isotropic
3
3D 1H-13C NOESY
1
13
2
isotropic
3
3D filtered NOESY
1
4
3
isotropic
3
2D 1H-1H NOESY
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Sample preparation
Details
Type
Solution-ID
Contents
Label
Solvent system
solution
1
0.5 mM [U-99% 15N][U-99% 13C; U-99% 15N] Sap1, 20 mM sodium phosphate, 90% H2O/10% D2O
15N/13C_sap1
90% H2O/10% D2O
solution
3
0.5 mM DNA (5'-CAAAACAATATT-3'), 20 mM sodium phosphate, 90% H2O/10% D2O
1H_DNA
90% H2O/10% D2O
solution
2
0.5 mM [U-99% 13C; U-99% 15N] Sap1, 0.7 mM DNA (5'-CAAAACAATATT-3'), 20 mM sodium phosphate, 90% H2O/10% D2O
15N/13C_complex
90% H2O/10% D2O
Sample
Conc. (mg/ml)
Component
Isotopic labeling
Solution-ID
0.5mM
Sap1
[U-99% 15N][U-99% 13C; U-99% 15N]
1
20mM
sodiumphosphate
naturalabundance
1
0.5mM
DNA (5'-CAAAACAATATT-3')
naturalabundance
3
20mM
sodiumphosphate
naturalabundance
3
0.5mM
Sap1
[U-99% 13C; U-99% 15N]
2
0.7mM
DNA (5'-CAAAACAATATT-3')
naturalabundance
2
20mM
sodiumphosphate
naturalabundance
2
Sample conditions
Ionic strength: 60 mM / Label: conditions_1 / pH: 6.0 / Pressure: 1 atm / Temperature: 298 K
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NMR measurement
NMR spectrometer
Type
Manufacturer
Model
Field strength (MHz)
Spectrometer-ID
Bruker AVANCE
Bruker
AVANCE
500
1
Bruker AVANCE
Bruker
AVANCE
800
2
Bruker AVANCE
Bruker
AVANCE
950
3
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Processing
NMR software
Name
Developer
Classification
X-PLOR NIH
Schwieters, Kuszewski, TjandraandClore
refinement
NMRView
Johnson, OneMoonScientific
chemicalshiftassignment
NMRPipe
Delaglio, Grzesiek, Vuister, Zhu, PfeiferandBax
processing
Refinement
Method: simulated annealing / Software ordinal: 2 Details: The structure model of the Sap1-DNA complex was derived based on the crystal structure of Sap1, the B-form DNA model based on the 3D-DART server, and the experimentally obtained inter- ...Details: The structure model of the Sap1-DNA complex was derived based on the crystal structure of Sap1, the B-form DNA model based on the 3D-DART server, and the experimentally obtained inter-molecular distance restraints from NMR NOESY spectra.
NMR representative
Selection criteria: lowest energy
NMR ensemble
Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 20
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