2FVT

NMR Structure of the Rpa2829 protein from Rhodopseudomonas palustris: Northeast Structural Genomics Target RpR43

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	4D_13C-separated_NOESY	1.2 mM Rpa2829 U-15N,13C; 20 mM ammonium acetate pH 5.0; 100 mM NaCl; 5mM CaCl2; 0.02% NaN3; 10 mM DTT; 95% H2O; 10% D2O	95% H2O; 10% D2O	100 mM NaCl; 5mM CaCl2; 20 mM Ammonium acetate	4.5	ambient	293
2	3D_13C-separated_NOESY	1.2 mM Rpa2829 U-15N,13C; 20 mM ammonium acetate pH 5.0; 100 mM NaCl; 5mM CaCl2; 0.02% NaN3; 10 mM DTT; 95% H2O; 10% D2O	95% H2O; 10% D2O	100 mM NaCl; 5mM CaCl2; 20 mM Ammonium acetate	5.0	ambient	293
3	3D_15N-separated_NOESY	1.2 mM Rpa2829 U-15N,13C; 20 mM ammonium acetate pH 5.0; 100 mM NaCl; 5mM CaCl2; 0.02% NaN3; 10 mM DTT; 95% H2O; 10% D2O	95% H2O; 10% D2O	100 mM NaCl; 5mM CaCl2; 20 mM Ammonium acetate	5.0	ambient	293
4	HNHA	1.2 mM Rpa2829 U-15N,13C; 20 mM ammonium acetate pH 5.0; 100 mM NaCl; 5mM CaCl2; 0.02% NaN3; 10 mM DTT; 95% H2O; 10% D2O	95% H2O; 10% D2O	100 mM NaCl; 5mM CaCl2; 20 mM Ammonium acetate	5.0	ambient	293

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Varian	INOVA	800
2	Varian	INOVA	750
3	Varian	INOVA	600
4	Varian	UNITYPLUS	500

NMR Refinement
Method	Details	Software
The initial structure was determined using automated structure determination (AutoStructure) and refined manually. A final refinement used simultated annealing in explicit solvent.	THE STRUCTURES ARE BASED ON A TOTAL OF 1039 RESTRAINTS. SUMMARY OF EXPERIMENTAL CONSTRAINTS: RESTRAINING DISTANCE RESTRAINTS: TOTAL = 864; INTRA-RESIDUE [I=J] = 160; SEQUENTIAL [(I-J)=1] = 225; MEDIUM RANGE [1<(I-J)<5] = 131; LONG RANGE [(I-J)>=5] = 348; HYDROGEN BOND RESTRAINTS = 72 (2 PER H-BOND); NUMBER OF RESTRAINING DISTANCE RESTRAINTS PER RESTRAINED RESIDUE = 8.2; DIHEDRAL-ANGLE RESTRAINTS = 103 (50 PHI, 52 PSI, 1 CHI-1); TOTAL NUMBER OF RESTRAINTS PER RESTRAINED RESIDUE = 8.9; NUMBER OF LONG RANGE NOE DISTANCE RESTRAINTS PER RESTRAINED RESIDUE = 3.0; NUMBER OF STRUCTURES COMPUTED = 30; NUMBER OF STRUCTURES USED = 20. AVERAGE DISTANCE VIOLATIONS >0.0001 ANG = 26.8+/-6; AVERAGE R.M.S. DISTANCE VIOLATION = 0.005 +/- 0.001 ANG; MAXIMUM NUMBER OF DISTANCE VIOLATIONS 39.MAXIMUM DISTANCE VIOLATION = 0.26 ANG; AVERAGE DIHEDRAL ANGLE VIOLATIONS: >0.0001 DEG = 3.3+/-1.3; MAX NUMBER OF DIHEDRAL ANGLE VIOLATIONS = 5; AVERAGE R.M.S. ANGLE VIOLATION = 0.42 +/- .01 DEG.; RMSD VALUES: BACKBONE ATOMS (N,C,C' RESIDUES 10-126) = 0.86 ANG, ALL HEAVY ATOMS = 1.52 ANG; BACKBONE ATOMS (N,C,C' RESIDUES 33-126) = 0.68 ANG, ALL HEAVY ATOMS = 1.1.38 ANG; BACKBONE ATOMS (N,C,C' RESIDUES 12-16,24-26,34-39,41-49,52-74,79-92,95-114,119-126) = 0.67 ANG,ALL HEAVY ATOMS = 1.19 ANG; PROCHECK (RESDIUES 10-126): MOST FAVORED REGIONS = 83.8%; ADDITIONAL ALLOWED REGIONS = 14.9%; GENEROUSLY ALLOWED REGIONS = 1.9%; DISALLOWED REGIONS = 0.4%.	VNMR

NMR Ensemble Information
Conformer Selection Criteria	structures with lowest energy and fewest restraint violations
Conformers Calculated Total Number	30
Conformers Submitted Total Number	20
Representative Model	1 (few violations and low energy and good geometery)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	collection	VNMR	6.1C	Varian
2	processing	Felix	98	MSI/Accelerys
3	data analysis	Sparky	3.106	Tom Goddard, Tom James
4	structure solution	AutoStructure	2.1.1	Janet Huang, G.T. Montelione
5	refinement	X-PLOR	NIH-XPLOR	A. Brunger
6	refinement	CNS	1.1	A. Brunger

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.