6UHW | pdb_00006uhw

Solution structure of an organic hydroperoxide resistance protein from Burkholderia pseudomallei. Seattle Structural Genomics Center for Infectious Disease target BupsA.00074.a.

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-15N HSQC	20 mM TRIS, 100 mM sodium chloride, 1 mM DTT, 1 mM [U-99% 13C; U-99% 15N] B74	93% H2O/7% D2O	0.12 M	7	1 atm	298	Varian VXRS 750
2	2D 1H-13C HSQC aliphatic	20 mM TRIS, 100 mM sodium chloride, 1 mM DTT, 1 mM [U-99% 13C; U-99% 15N] B74	93% H2O/7% D2O	0.12 M	7	1 atm	298	Bruker AVANCE II 750
3	2D 1H-15N HSQC	20 mM TRIS, 100 mM sodium chloride, 1 mM DTT, 1 mM 99% 13C; U-99% 15N] B74	99% D2O	0.12 M	7	1 atm	298	Bruker AVANCE II 750
4	3D C(CO)NH	20 mM TRIS, 100 mM sodium chloride, 1 mM DTT, 1 mM 99% 13C; U-99% 15N; 50%-2H]] B74	93% H2O/7% D2O	0.12 M	7	1 atm	298	Varian VXRS 750
5	3D HNCACB	20 mM TRIS, 100 mM sodium chloride, 1 mM DTT, 1 mM 99% 13C; U-99% 15N; 50%-2H]] B74	93% H2O/7% D2O	0.12 M	7	1 atm	298	Varian VXRS 750
12	3D HCCH-TOCSY	20 mM TRIS, 100 mM sodium chloride, 1 mM DTT, 1 mM 99% 13C; U-99% 15N; 50%-2H]] B74	93% H2O/7% D2O	0.12 M	7	1 atm	298	Varian VXRS 600
11	3D 1H-15N NOESY	20 mM TRIS, 100 mM sodium chloride, 1 mM DTT, 1 mM [U-99% 13C; U-99% 15N] B74	93% H2O/7% D2O	0.12 M	7	1 atm	298	Varian VXRS 750
10	3D 1H-13C NOESY aromatic	20 mM TRIS, 100 mM sodium chloride, 1 mM DTT, 1 mM [U-99% 13C; U-99% 15N] B74	93% H2O/7% D2O	0.12 M	7	1 atm	298	Varian VXRS 750
9	3D 1H-13C NOESY aliphatic	20 mM TRIS, 100 mM sodium chloride, 1 mM DTT, 1 mM 99% 13C; U-99% 15N] B74	99% D2O	0.12 M	7	1 atm	298	Bruker AVANCE II 750
8	3D 1H-13C NOESY aliphatic	20 mM TRIS, 100 mM sodium chloride, 1 mM DTT, 1 mM [U-99% 13C; U-99% 15N] B74	93% H2O/7% D2O	0.12 M	7	1 atm	298	Varian VXRS 750
7	3D HNCO	20 mM TRIS, 100 mM sodium chloride, 1 mM DTT, 1 mM [U-99% 13C; U-99% 15N] B74	93% H2O/7% D2O	0.12 M	7	1 atm	298	Varian VXRS 600
6	3D HNCA	20 mM TRIS, 100 mM sodium chloride, 1 mM DTT, 1 mM 99% 13C; U-99% 15N; 50%-2H]] B74	93% H2O/7% D2O	0.12 M	7	1 atm	298	Varian VXRS 600
13	2D 1H-15N HSQC	20 mM TRIS, 100 mM sodium chloride, 1 mM DTT, 1 mM 99% 13C; U-99% 15N] B74	99% D2O	0.12 M	7	1 atm	298	Bruker AVANCE II 750
14	3D H(CCO)NH	20 mM TRIS, 100 mM sodium chloride, 1 mM DTT, 1 mM 99% 13C; U-99% 15N; 50%-2H]] B74	93% H2O/7% D2O	0.12 M	7	1 atm	298	Varian VXRS 600
15	2D 1H-13C HSQC aliphatic	20 mM TRIS, 100 mM sodium chloride, 1 mM DTT, 1 mM [U-10% 13C; U-99% 15N] B74	93% H2O/7% D2O	0.12 M	7	1 atm	298	Bruker AVANCE II 750
16	2D 1H-13C HSQC aromatic	20 mM TRIS, 100 mM sodium chloride, 1 mM DTT, 1 mM [U-99% 13C; U-99% 15N] B74	93% H2O/7% D2O	0.12 M	7	1 atm	298	Varian VXRS 750

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE II	750
2	Varian	VXRS	750
4	Varian	VXRS	600

NMR Refinement
Method	Details	Software
torsion angle dynamics	Thirty-four pairs of intermolecular molecule distance restraints, identified with the assistance of homology models and confirmed in the NOE data, were introduced to coax the structure into a dimeric structure using CYANA. 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	CYANA

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	processing	Felix	2007	Accelrys Software Inc.
2	refinement	CYANA	2.1	Guntert, Mumenthaler and Wuthrich
3	chemical shift assignment	Sparky	3.115	Goddard
4	peak picking	Sparky	3.115	Goddard
5	data analysis	Sparky	3.115	Goddard
6	data analysis	TALOS	+	Cornilescu, Delaglio and Bax
7	data analysis	PSVS	1.5	Bhattacharya and Montelione
8	structure calculation	CYANA		Guntert, Mumenthaler and Wuthrich

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.