9DCN | pdb_00009dcn

Solution structure of the translation initiation factor IF-1 from Neisseria gonorrhoeae (NCCP11945). Seattle Structural Genomics Center for Infectious Disease target NegoA.17902.a

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-13C HSQC aliphatic	200 mM sodium chloride, 20 mM TRIS, 1 mM EDTA, 1 mM DTT, 0.8 mM [U-98% 13C; U-98% 15N] R20	93% H2O/7% D2O	222 mM	7	1 atm	293	Bruker Ascend 700
2	2D 1H-15N HSQC	200 mM sodium chloride, 20 mM TRIS, 1 mM EDTA, 1 mM DTT, 0.8 mM [U-98% 13C; U-98% 15N] R20	93% H2O/7% D2O	222 mM	7	1 atm	293	Bruker Ascend 700
3	3D 1H-13C NOESY aliphatic	200 mM sodium chloride, 20 mM TRIS, 1 mM EDTA, 1 mM DTT, 0.8 mM [U-98% 13C; U-98% 15N] R20	93% H2O/7% D2O	222 mM	7	1 atm	293	Bruker Ascend 700
4	3D 1H-13C NOESY aromatic	200 mM sodium chloride, 20 mM TRIS, 1 mM EDTA, 1 mM DTT, 0.8 mM [U-98% 13C; U-98% 15N] R20	93% H2O/7% D2O	222 mM	7	1 atm	293	Bruker Ascend 700
5	3D 1H-15N NOESY	200 mM sodium chloride, 20 mM TRIS, 1 mM EDTA, 1 mM DTT, 0.8 mM [U-98% 13C; U-98% 15N] R20	93% H2O/7% D2O	222 mM	7	1 atm	293	Bruker Ascend 700
12	3D 1H-15N TOCSY	200 mM sodium chloride, 20 mM TRIS, 1 mM EDTA, 1 mM DTT, 0.8 mM [U-98% 13C; U-98% 15N] R20	93% H2O/7% D2O	222 mM	7	1 atm	293	Bruker Ascend 700
11	3D C(CO)NH	200 mM sodium chloride, 20 mM TRIS, 1 mM EDTA, 1 mM DTT, 0.8 mM [U-98% 13C; U-98% 15N] R20	93% H2O/7% D2O	222 mM	7	1 atm	293	Bruker Ascend 700
10	3D HNCACB	200 mM sodium chloride, 20 mM TRIS, 1 mM EDTA, 1 mM DTT, 0.8 mM [U-98% 13C; U-98% 15N] R20	93% H2O/7% D2O	222 mM	7	1 atm	293	Bruker Ascend 700
9	3D CBCA(CO)NH	200 mM sodium chloride, 20 mM TRIS, 1 mM EDTA, 1 mM DTT, 0.8 mM [U-98% 13C; U-98% 15N] R20	93% H2O/7% D2O	222 mM	7	1 atm	293	Bruker Ascend 700
8	3D HNCO	200 mM sodium chloride, 20 mM TRIS, 1 mM EDTA, 1 mM DTT, 0.8 mM [U-98% 13C; U-98% 15N] R20	93% H2O/7% D2O	222 mM	7	1 atm	293	Bruker Ascend 700
7	2D 1H-15N HSQC Deuterium Exchange	200 mM sodium chloride, 20 mM TRIS, 1 mM EDTA, 1 mM DTT, 0.2 mM [U-10% 13C; U-99% 15N] R20	100% D2O	222 mM	7	1 atm	293	Bruker Ascend 700
6	2D 1H-13C HSQC aliphatic	200 mM sodium chloride, 20 mM TRIS, 1 mM EDTA, 1 mM DTT, 0.2 mM [U-10% 13C; U-99% 15N] R20	100% D2O	222 mM	7	1 atm	293	Bruker Ascend 700

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	Ascend	700

NMR Refinement
Method	Details	Software
torsion angle dynamics		CYANA
molecular dynamics	Water Refinement. STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING CYANA (AUTOMATED NOESY ASSIGNMENTS). A TOTAL OF 20 STRUCTURES OUT OF 100 WITH LOWEST TARGET FUNCTION FROM THE FINAL CYANA CALCULATION WERE TAKEN AND REFINED BY RESTRAINED MOLECULAR DYNAMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS) AFTER ADDING 0% TO THE UPPER BOUNDARY LIMIT OF THE DISTANCE RESTRAINTS AND THE VDW. Only 8 slowly exchanging amide resonances observed in the deuterium exchange experiment. Other hydrogen bonds introduced on the basis of proximity in early structure calculations (after addition of dihedral angle restraints).	CNS

NMR Ensemble Information
Conformer Selection Criteria	target function
Conformers Calculated Total Number	100
Conformers Submitted Total Number	20
Representative Model	1 (closest to the average)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	structure calculation	CYANA	1.2	Guntert, Mumenthaler and Wuthrich
2	refinement	CNS	SOLVE 1.3	Brunger, Adams, Clore, Gros, Nilges and Read
3	chemical shift assignment	Poky		Manthey, Tonelli, Clos II, Rahimi, Markley and Lee
4	processing	NMRPipe		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
5	data analysis	TALOS+		Yang Shen, Frank Delaglio, Gabriel Cornilescu, and Ad Bax

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.