2KCT

Solution nmr structure of the ob-fold domain of heme chaperone ccme from desulfovibrio vulgaris. northeast structural genomics target dvr115g.

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-15N HSQC	1.3 mM [U-100% 13C; U-100% 15N] DvR115G, 20 mM ammonium acetate, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O	0.2	4.5	AMBIENT	298
2	2D 1H-13C HSQC	1.3 mM [U-100% 13C; U-100% 15N] DvR115G, 20 mM ammonium acetate, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O	0.2	4.5	AMBIENT	298
3	3D SIMULTANEOUS CN NOESY	1.3 mM [U-100% 13C; U-100% 15N] DvR115G, 20 mM ammonium acetate, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O	0.2	4.5	AMBIENT	298
4	3D 1H-13C NOESY aromatic	1.3 mM [U-100% 13C; U-100% 15N] DvR115G, 20 mM ammonium acetate, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O	0.2	4.5	AMBIENT	298
5	2D 1H-13C HSQC HIGH RES. (L/V METHYL STEREOASSIGNMENT)	1.3 mM [U-100% 13C; U-100% 15N] DvR115G, 20 mM ammonium acetate, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O	0.2	4.5	AMBIENT	298
6	3D HNCO	1.3 mM [U-100% 13C; U-100% 15N] DvR115G, 20 mM ammonium acetate, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O	0.2	4.5	AMBIENT	298
7	3D HN(CO)CA	1.3 mM [U-100% 13C; U-100% 15N] DvR115G, 20 mM ammonium acetate, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O	0.2	4.5	AMBIENT	298
8	3D CBCA(CO)NH	1.3 mM [U-100% 13C; U-100% 15N] DvR115G, 20 mM ammonium acetate, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O	0.2	4.5	AMBIENT	298
9	3D HNCACB	1.3 mM [U-100% 13C; U-100% 15N] DvR115G, 20 mM ammonium acetate, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O	0.2	4.5	AMBIENT	298
10	3D HBHA(CO)NH	1.3 mM [U-100% 13C; U-100% 15N] DvR115G, 20 mM ammonium acetate, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O	0.2	4.5	AMBIENT	298
11	3D HN(CA)CO	1.3 mM [U-100% 13C; U-100% 15N] DvR115G, 20 mM ammonium acetate, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O	0.2	4.5	AMBIENT	298
12	3D C(CO)NH TOCSY	1.3 mM [U-100% 13C; U-100% 15N] DvR115G, 20 mM ammonium acetate, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O	0.2	4.5	AMBIENT	298
13	3D HCCH-COSY ALIPHATIC	1.3 mM [U-100% 13C; U-100% 15N] DvR115G, 20 mM ammonium acetate, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O	0.2	4.5	AMBIENT	298
14	3D HCCH- TOCSY ALIPHATIC	1.3 mM [U-100% 13C; U-100% 15N] DvR115G, 20 mM ammonium acetate, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O	0.2	4.5	AMBIENT	298
15	3D (H)CCH- TOCSY ALIPHATIC	1.3 mM [U-100% 13C; U-100% 15N] DvR115G, 20 mM ammonium acetate, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O	0.2	4.5	AMBIENT	298
16	3D HNHA	1.3 mM [U-100% 13C; U-100% 15N] DvR115G, 20 mM ammonium acetate, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O	0.2	4.5	AMBIENT	298
17	2D 1H-15N HETNOE	1.3 mM [U-100% 13C; U-100% 15N] DvR115G, 20 mM ammonium acetate, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O	0.2	4.5	AMBIENT	298
18	1D 1H-15N T1 AND T2	1.3 mM [U-100% 13C; U-100% 15N] DvR115G, 20 mM ammonium acetate, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS	90% H2O/10% D2O	0.2	4.5	AMBIENT	298
19	2D 1H-15N TROSY (for N-H RDC's)	10 % [U-5% 13C; U-100% 15N] DvR115G, 4.2 % PEG/hexanol	95% H2O/5% D2O	0.2	4.5	AMBIENT	298

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE	800
2	Varian	INOVA	600

NMR Refinement
Method	Details	Software
simulated annealing	THE FINAL STRUCTURES ARE BASED ON A TOTAL OF 1384 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS AND 79 DIHEDRAL ANGLE CONSTRAINTS; 0 HYDROGEN BOND CONSTRAINTS (16.8 CONSTRAINTS PER RESIDUE, 6.0 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 43 TO 130 BY PSVS 1.3). IN ADDITION, 49 RESOLVED N-H RESIDUAL DIPOLAR COUPLINGS FOR ORDERED RESIDUES WERE INCLUDED IN ALL STRUCTURE CALCULATIONS. STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING CYANA 3.0. THE 20 STRUCTURES OUT OF 100 WITH THE LOWEST TARGET FUNCTION WERE FURTHER REFINED BY RESTRAINED MOLECULAR DYNAMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS) WITH PARAM19.	CNS

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	100
Conformers Submitted Total Number	20
Representative Model	1 (n/a)

Additional NMR Experimental Information
Details	THE PROTEIN IS MONOMERIC BY GEL FILTRATION CHROMATOGRAPHY, STATIC LIGHT SCATTERING AND 15N T1/T2 RELAXATION. THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATED BACKBONE ASSIGNMENTS WERE MADE USING AUTOASSIGN AND PINE, AND THE SIDE CHAIN ASSIGNMENTS WERE COMPLETED MANUALLY. AUTOMATIC NOESY ASSIGNMENTS WERE DETERMINED USING CYANA 3.0. BACKBONE (PHI/ PSI) DIHEDRAL ANGLE CONSTRAINTS WERE OBTAINED FROM TALOS. ROTAMER STATES OF SPECIFIC ORDERED RESIDUES WERE CONSTRAINED IN THE FINAL STAGE OF THE STRUCTURE REFINEMENT BASED ON PROCHECK. COMPLETENESS OF NMR ASSIGNMENTS (EXCLUDING C- TERMINAL HHHHHH): BACKBONE, 98.6%, SIDE CHAIN, 97.2%, AROMATICS, 100%, STEREOSPECIFIC METHYL, 100%, STEREOSPECIFIC SIDE CHAIN NH2: 100%. FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUES 43 TO 130, PSVS 1.3), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE: 52-67,70-79,86-112,115-127: (A) RMSD (ORDERED RESIDUES): BB, 0.5, HEAVY ATOM, 0.9. (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 93.9%, ADDITIONALLY ALLOWED, 6.1%, GENEROUSLY ALLOWED, 0.0%, DISALLOWED, 0.0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, -0.62/-2.12, ALL, -0.43/-2.54. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 10.87/-0.34 (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (RESIDUES 43-130): RECALL, 0.984, PRECISION, 0.915, F-MEASURE, 0.948, DP-SCORE, 0.795. (F) NUMBER OF CLOSE CONTACTS PER 20 MODELS: 4. (G) AGREEMENT WITH RESIDUAL DIPOLAR COUPLINGS (20 MODELS): CORRELATION COEFFICIENT (R): 0.995 (0.001); Q RMS: 0.096 (0.011). THE C- TERMINAL HIS TAG RESIDUES OF THE PROTEIN (HHHHHH) WERE NOT INCLUDED IN THE STRUCTURE CALCULATIONS AND HAVE BEEN OMITTED FROM THIS DEPOSITION. COORDINATES FOR THE FOLLOWING RESIDUES ARE NOT WELL DETERMINED [S(PHI) + S(PSI) < 1.8]: 43-51,68-69, 80-85,113-114,128-130.

Additional NMR Experimental Information

Details

THE PROTEIN IS MONOMERIC BY GEL FILTRATION CHROMATOGRAPHY, STATIC LIGHT SCATTERING AND 15N T1/T2 RELAXATION. THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATED BACKBONE ASSIGNMENTS WERE MADE USING AUTOASSIGN AND PINE, AND THE SIDE CHAIN ASSIGNMENTS WERE COMPLETED MANUALLY. AUTOMATIC NOESY ASSIGNMENTS WERE DETERMINED USING CYANA 3.0. BACKBONE (PHI/ PSI) DIHEDRAL ANGLE CONSTRAINTS WERE OBTAINED FROM TALOS. ROTAMER STATES OF SPECIFIC ORDERED RESIDUES WERE CONSTRAINED IN THE FINAL STAGE OF THE STRUCTURE REFINEMENT BASED ON PROCHECK. COMPLETENESS OF NMR ASSIGNMENTS (EXCLUDING C- TERMINAL HHHHHH): BACKBONE, 98.6%, SIDE CHAIN, 97.2%, AROMATICS, 100%, STEREOSPECIFIC METHYL, 100%, STEREOSPECIFIC SIDE CHAIN NH2: 100%. FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUES 43 TO 130, PSVS 1.3), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE: 52-67,70-79,86-112,115-127: (A) RMSD (ORDERED RESIDUES): BB, 0.5, HEAVY ATOM, 0.9. (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 93.9%, ADDITIONALLY ALLOWED, 6.1%, GENEROUSLY ALLOWED, 0.0%, DISALLOWED, 0.0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, -0.62/-2.12, ALL, -0.43/-2.54. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 10.87/-0.34 (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (RESIDUES 43-130): RECALL, 0.984, PRECISION, 0.915, F-MEASURE, 0.948, DP-SCORE, 0.795. (F) NUMBER OF CLOSE CONTACTS PER 20 MODELS: 4. (G) AGREEMENT WITH RESIDUAL DIPOLAR COUPLINGS (20 MODELS): CORRELATION COEFFICIENT (R): 0.995 (0.001); Q RMS: 0.096 (0.011). THE C- TERMINAL HIS TAG RESIDUES OF THE PROTEIN (HHHHHH) WERE NOT INCLUDED IN THE STRUCTURE CALCULATIONS AND HAVE BEEN OMITTED FROM THIS DEPOSITION. COORDINATES FOR THE FOLLOWING RESIDUES ARE NOT WELL DETERMINED [S(PHI) + S(PSI) < 1.8]: 43-51,68-69, 80-85,113-114,128-130.

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	refinement	CNS	1.1	BRUNGER, ADAMS, CLORE, GROS, NILGES
2	structure solution	TopSpin	2.1
3	structure solution	VnmrJ	2.1B
4	structure solution	NMRPipe	2.3
5	structure solution	Sparky	3.112
6	structure solution	PINE
7	structure solution	AutoAssign	2.4.0
8	structure solution	CYANA	3.0
9	structure solution	AutoStructure	2.2.1
10	structure solution	PSVS	1.3
11	structure solution	PdbStat	5.1
12	structure solution	PALES

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.

Prepare Data

Validate Data

Deposit Data

Help and Resources

2KCT

Solution nmr structure of the ob-fold domain of heme chaperone ccme from desulfovibrio vulgaris. northeast structural genomics target dvr115g.