2K52

Structure of uncharacterized protein MJ1198 from Methanocaldococcus jannaschii. Northeast Structural Genomics Target MjR117B

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-15N HSQC	1.682 MM [U-100% 13C 15N] MJR117B, 20 MM AMMONIUM ACETATE, 100 MM SODIUM CHLORIDE, 0.02 MM SODIUM AZIDE, 10 MM DTT, 50 UM DSS, 5 MM CALCIUM CHLORIDE, 1X PROTEASE INHIBITOR, 90% H2O/ 10% D2O; 1.226 MM [5% 13C; U- 100% 15N] MJR117B, 20 MM AMMONIUM ACETATE, 100 MM SODIUM CHLORIDE, 0.02 MM SODIUM AZIDE, 10 MM DTT, 50 UM DSS, 5 MM CALCIUM CHLORIDE, 1X PROTEASE INHIBITOR, 90% H2O/ 10% D2O		0.1	4.5	AMBIENT	298
2	2D 1H-13C HSQC	1.682 MM [U-100% 13C 15N] MJR117B, 20 MM AMMONIUM ACETATE, 100 MM SODIUM CHLORIDE, 0.02 MM SODIUM AZIDE, 10 MM DTT, 50 UM DSS, 5 MM CALCIUM CHLORIDE, 1X PROTEASE INHIBITOR, 90% H2O/ 10% D2O; 1.226 MM [5% 13C; U- 100% 15N] MJR117B, 20 MM AMMONIUM ACETATE, 100 MM SODIUM CHLORIDE, 0.02 MM SODIUM AZIDE, 10 MM DTT, 50 UM DSS, 5 MM CALCIUM CHLORIDE, 1X PROTEASE INHIBITOR, 90% H2O/ 10% D2O		0.1	4.5	AMBIENT	298
3	3D CBCA(CO)NH	1.682 MM [U-100% 13C 15N] MJR117B, 20 MM AMMONIUM ACETATE, 100 MM SODIUM CHLORIDE, 0.02 MM SODIUM AZIDE, 10 MM DTT, 50 UM DSS, 5 MM CALCIUM CHLORIDE, 1X PROTEASE INHIBITOR, 90% H2O/ 10% D2O; 1.226 MM [5% 13C; U- 100% 15N] MJR117B, 20 MM AMMONIUM ACETATE, 100 MM SODIUM CHLORIDE, 0.02 MM SODIUM AZIDE, 10 MM DTT, 50 UM DSS, 5 MM CALCIUM CHLORIDE, 1X PROTEASE INHIBITOR, 90% H2O/ 10% D2O		0.1	4.5	AMBIENT	298
4	3D HNCO	1.682 MM [U-100% 13C 15N] MJR117B, 20 MM AMMONIUM ACETATE, 100 MM SODIUM CHLORIDE, 0.02 MM SODIUM AZIDE, 10 MM DTT, 50 UM DSS, 5 MM CALCIUM CHLORIDE, 1X PROTEASE INHIBITOR, 90% H2O/ 10% D2O; 1.226 MM [5% 13C; U- 100% 15N] MJR117B, 20 MM AMMONIUM ACETATE, 100 MM SODIUM CHLORIDE, 0.02 MM SODIUM AZIDE, 10 MM DTT, 50 UM DSS, 5 MM CALCIUM CHLORIDE, 1X PROTEASE INHIBITOR, 90% H2O/ 10% D2O		0.1	4.5	AMBIENT	298
5	3D HN(CO)CA	1.682 MM [U-100% 13C 15N] MJR117B, 20 MM AMMONIUM ACETATE, 100 MM SODIUM CHLORIDE, 0.02 MM SODIUM AZIDE, 10 MM DTT, 50 UM DSS, 5 MM CALCIUM CHLORIDE, 1X PROTEASE INHIBITOR, 90% H2O/ 10% D2O; 1.226 MM [5% 13C; U- 100% 15N] MJR117B, 20 MM AMMONIUM ACETATE, 100 MM SODIUM CHLORIDE, 0.02 MM SODIUM AZIDE, 10 MM DTT, 50 UM DSS, 5 MM CALCIUM CHLORIDE, 1X PROTEASE INHIBITOR, 90% H2O/ 10% D2O		0.1	4.5	AMBIENT	298
6	3D HBHA(CO)NH	1.682 MM [U-100% 13C 15N] MJR117B, 20 MM AMMONIUM ACETATE, 100 MM SODIUM CHLORIDE, 0.02 MM SODIUM AZIDE, 10 MM DTT, 50 UM DSS, 5 MM CALCIUM CHLORIDE, 1X PROTEASE INHIBITOR, 90% H2O/ 10% D2O; 1.226 MM [5% 13C; U- 100% 15N] MJR117B, 20 MM AMMONIUM ACETATE, 100 MM SODIUM CHLORIDE, 0.02 MM SODIUM AZIDE, 10 MM DTT, 50 UM DSS, 5 MM CALCIUM CHLORIDE, 1X PROTEASE INHIBITOR, 90% H2O/ 10% D2O		0.1	4.5	AMBIENT	298
7	3D HNCACB	1.682 MM [U-100% 13C 15N] MJR117B, 20 MM AMMONIUM ACETATE, 100 MM SODIUM CHLORIDE, 0.02 MM SODIUM AZIDE, 10 MM DTT, 50 UM DSS, 5 MM CALCIUM CHLORIDE, 1X PROTEASE INHIBITOR, 90% H2O/ 10% D2O; 1.226 MM [5% 13C; U- 100% 15N] MJR117B, 20 MM AMMONIUM ACETATE, 100 MM SODIUM CHLORIDE, 0.02 MM SODIUM AZIDE, 10 MM DTT, 50 UM DSS, 5 MM CALCIUM CHLORIDE, 1X PROTEASE INHIBITOR, 90% H2O/ 10% D2O		0.1	4.5	AMBIENT	298
8	3D HN(CA)CO	1.682 MM [U-100% 13C 15N] MJR117B, 20 MM AMMONIUM ACETATE, 100 MM SODIUM CHLORIDE, 0.02 MM SODIUM AZIDE, 10 MM DTT, 50 UM DSS, 5 MM CALCIUM CHLORIDE, 1X PROTEASE INHIBITOR, 90% H2O/ 10% D2O; 1.226 MM [5% 13C; U- 100% 15N] MJR117B, 20 MM AMMONIUM ACETATE, 100 MM SODIUM CHLORIDE, 0.02 MM SODIUM AZIDE, 10 MM DTT, 50 UM DSS, 5 MM CALCIUM CHLORIDE, 1X PROTEASE INHIBITOR, 90% H2O/ 10% D2O		0.1	4.5	AMBIENT	298
9	3D HCCH-TOCSY	1.682 MM [U-100% 13C 15N] MJR117B, 20 MM AMMONIUM ACETATE, 100 MM SODIUM CHLORIDE, 0.02 MM SODIUM AZIDE, 10 MM DTT, 50 UM DSS, 5 MM CALCIUM CHLORIDE, 1X PROTEASE INHIBITOR, 90% H2O/ 10% D2O; 1.226 MM [5% 13C; U- 100% 15N] MJR117B, 20 MM AMMONIUM ACETATE, 100 MM SODIUM CHLORIDE, 0.02 MM SODIUM AZIDE, 10 MM DTT, 50 UM DSS, 5 MM CALCIUM CHLORIDE, 1X PROTEASE INHIBITOR, 90% H2O/ 10% D2O		0.1	4.5	AMBIENT	298
10	3D HCCH-COSY	1.682 MM [U-100% 13C 15N] MJR117B, 20 MM AMMONIUM ACETATE, 100 MM SODIUM CHLORIDE, 0.02 MM SODIUM AZIDE, 10 MM DTT, 50 UM DSS, 5 MM CALCIUM CHLORIDE, 1X PROTEASE INHIBITOR, 90% H2O/ 10% D2O; 1.226 MM [5% 13C; U- 100% 15N] MJR117B, 20 MM AMMONIUM ACETATE, 100 MM SODIUM CHLORIDE, 0.02 MM SODIUM AZIDE, 10 MM DTT, 50 UM DSS, 5 MM CALCIUM CHLORIDE, 1X PROTEASE INHIBITOR, 90% H2O/ 10% D2O		0.1	4.5	AMBIENT	298
11	3D CCH- TOCSY	1.682 MM [U-100% 13C 15N] MJR117B, 20 MM AMMONIUM ACETATE, 100 MM SODIUM CHLORIDE, 0.02 MM SODIUM AZIDE, 10 MM DTT, 50 UM DSS, 5 MM CALCIUM CHLORIDE, 1X PROTEASE INHIBITOR, 90% H2O/ 10% D2O; 1.226 MM [5% 13C; U- 100% 15N] MJR117B, 20 MM AMMONIUM ACETATE, 100 MM SODIUM CHLORIDE, 0.02 MM SODIUM AZIDE, 10 MM DTT, 50 UM DSS, 5 MM CALCIUM CHLORIDE, 1X PROTEASE INHIBITOR, 90% H2O/ 10% D2O		0.1	4.5	AMBIENT	298
12	3D SIM 13C	1.682 MM [U-100% 13C 15N] MJR117B, 20 MM AMMONIUM ACETATE, 100 MM SODIUM CHLORIDE, 0.02 MM SODIUM AZIDE, 10 MM DTT, 50 UM DSS, 5 MM CALCIUM CHLORIDE, 1X PROTEASE INHIBITOR, 90% H2O/ 10% D2O; 1.226 MM [5% 13C; U- 100% 15N] MJR117B, 20 MM AMMONIUM ACETATE, 100 MM SODIUM CHLORIDE, 0.02 MM SODIUM AZIDE, 10 MM DTT, 50 UM DSS, 5 MM CALCIUM CHLORIDE, 1X PROTEASE INHIBITOR, 90% H2O/ 10% D2O		0.1	4.5	AMBIENT	298
13	15N NOESY	1.682 MM [U-100% 13C 15N] MJR117B, 20 MM AMMONIUM ACETATE, 100 MM SODIUM CHLORIDE, 0.02 MM SODIUM AZIDE, 10 MM DTT, 50 UM DSS, 5 MM CALCIUM CHLORIDE, 1X PROTEASE INHIBITOR, 90% H2O/ 10% D2O; 1.226 MM [5% 13C; U- 100% 15N] MJR117B, 20 MM AMMONIUM ACETATE, 100 MM SODIUM CHLORIDE, 0.02 MM SODIUM AZIDE, 10 MM DTT, 50 UM DSS, 5 MM CALCIUM CHLORIDE, 1X PROTEASE INHIBITOR, 90% H2O/ 10% D2O		0.1	4.5	AMBIENT	298
14	3D ARO 13C NOESY	1.682 MM [U-100% 13C 15N] MJR117B, 20 MM AMMONIUM ACETATE, 100 MM SODIUM CHLORIDE, 0.02 MM SODIUM AZIDE, 10 MM DTT, 50 UM DSS, 5 MM CALCIUM CHLORIDE, 1X PROTEASE INHIBITOR, 90% H2O/ 10% D2O; 1.226 MM [5% 13C; U- 100% 15N] MJR117B, 20 MM AMMONIUM ACETATE, 100 MM SODIUM CHLORIDE, 0.02 MM SODIUM AZIDE, 10 MM DTT, 50 UM DSS, 5 MM CALCIUM CHLORIDE, 1X PROTEASE INHIBITOR, 90% H2O/ 10% D2O		0.1	4.5	AMBIENT	298
15	2D 1H-13C HSQC STEREO	1.682 MM [U-100% 13C 15N] MJR117B, 20 MM AMMONIUM ACETATE, 100 MM SODIUM CHLORIDE, 0.02 MM SODIUM AZIDE, 10 MM DTT, 50 UM DSS, 5 MM CALCIUM CHLORIDE, 1X PROTEASE INHIBITOR, 90% H2O/ 10% D2O; 1.226 MM [5% 13C; U- 100% 15N] MJR117B, 20 MM AMMONIUM ACETATE, 100 MM SODIUM CHLORIDE, 0.02 MM SODIUM AZIDE, 10 MM DTT, 50 UM DSS, 5 MM CALCIUM CHLORIDE, 1X PROTEASE INHIBITOR, 90% H2O/ 10% D2O		0.1	4.5	AMBIENT	298
16	2D HETNOE	1.682 MM [U-100% 13C 15N] MJR117B, 20 MM AMMONIUM ACETATE, 100 MM SODIUM CHLORIDE, 0.02 MM SODIUM AZIDE, 10 MM DTT, 50 UM DSS, 5 MM CALCIUM CHLORIDE, 1X PROTEASE INHIBITOR, 90% H2O/ 10% D2O; 1.226 MM [5% 13C; U- 100% 15N] MJR117B, 20 MM AMMONIUM ACETATE, 100 MM SODIUM CHLORIDE, 0.02 MM SODIUM AZIDE, 10 MM DTT, 50 UM DSS, 5 MM CALCIUM CHLORIDE, 1X PROTEASE INHIBITOR, 90% H2O/ 10% D2O		0.1	4.5	AMBIENT	298
17	PSEUDO 2D N15 T1	1.682 MM [U-100% 13C 15N] MJR117B, 20 MM AMMONIUM ACETATE, 100 MM SODIUM CHLORIDE, 0.02 MM SODIUM AZIDE, 10 MM DTT, 50 UM DSS, 5 MM CALCIUM CHLORIDE, 1X PROTEASE INHIBITOR, 90% H2O/ 10% D2O; 1.226 MM [5% 13C; U- 100% 15N] MJR117B, 20 MM AMMONIUM ACETATE, 100 MM SODIUM CHLORIDE, 0.02 MM SODIUM AZIDE, 10 MM DTT, 50 UM DSS, 5 MM CALCIUM CHLORIDE, 1X PROTEASE INHIBITOR, 90% H2O/ 10% D2O		0.1	4.5	AMBIENT	298
18	PSEUDO 2D N15 T2 (CPMG)	1.682 MM [U-100% 13C 15N] MJR117B, 20 MM AMMONIUM ACETATE, 100 MM SODIUM CHLORIDE, 0.02 MM SODIUM AZIDE, 10 MM DTT, 50 UM DSS, 5 MM CALCIUM CHLORIDE, 1X PROTEASE INHIBITOR, 90% H2O/ 10% D2O; 1.226 MM [5% 13C; U- 100% 15N] MJR117B, 20 MM AMMONIUM ACETATE, 100 MM SODIUM CHLORIDE, 0.02 MM SODIUM AZIDE, 10 MM DTT, 50 UM DSS, 5 MM CALCIUM CHLORIDE, 1X PROTEASE INHIBITOR, 90% H2O/ 10% D2O		0.1	4.5	AMBIENT	298
19	2D 1H-13C HSQC CT ARO	1.682 MM [U-100% 13C 15N] MJR117B, 20 MM AMMONIUM ACETATE, 100 MM SODIUM CHLORIDE, 0.02 MM SODIUM AZIDE, 10 MM DTT, 50 UM DSS, 5 MM CALCIUM CHLORIDE, 1X PROTEASE INHIBITOR, 90% H2O/ 10% D2O; 1.226 MM [5% 13C; U- 100% 15N] MJR117B, 20 MM AMMONIUM ACETATE, 100 MM SODIUM CHLORIDE, 0.02 MM SODIUM AZIDE, 10 MM DTT, 50 UM DSS, 5 MM CALCIUM CHLORIDE, 1X PROTEASE INHIBITOR, 90% H2O/ 10% D2O		0.1	4.5	AMBIENT	298

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

NMR Refinement
Method	Details	Software
torsion angle dynamics		CNS

NMR Ensemble Information
Conformer Selection Criteria	target function
Conformers Calculated Total Number	100
Conformers Submitted Total Number	20
Representative Model	1 (n/a)

Additional NMR Experimental Information
Details	MONOMER BY GEL FILTRATION CHROMATOGRAPHY/LIGHT SCATTERING AND BY NMR. T1/T2 (MS) = 792.1/78.18, TAUC = 9.7(NS) CONSISTENT WITH MOLECULAR WEIGHT. STRUCTURE DETERMINED BY TRIPLE RESONANCE NMR SPECTROSCOPY. NOESY ASSIGNMENTS BY CYANA2.1. 20 OF 100 STRUCTURES LOWEST TARGET FUNCTION SELECTED WITH CYANA2.1. SELECTED MODELS ARE FURTHER REFINED USING CNS IN EXPLICIT WATER SHELL (NILGES PROTOCOL WITH PARAM19). ASSIGNMENT STATS AROMATIC (SC) 92.6%, VL METHYL STEREOSPECIFIC 100%, UNAMBIGUOS SIDECHAIN NH2 100%. STRUCTURE BASED ON 1088 NOE, 166 DIHE. MAX NOE VIOLATION: 0.25 A (1MODEL); MAX DIHE VIOLATION: 3.2 DEG. 2 TOTAL CLOSE CONTACTS PER 20 MODELS. STRUCTURE QUALITY FACTOR > 1.8. SECONDARY STRUCTURE - BETA STRANDS: (8-17, 20-26, 29- 33, 51-60, 65-70). RMSD 0.4 BACKBONE, 0.8 ALL HEAVY ATOMS. MOLPROBITY CLASH: 16.80/-1.36 (RAW/Z). RPF SCORES ALL ASSIGNED PRECISION: 0.89, F-MEASURE: 0.93, DP-SCORE: 0.83.

Additional NMR Experimental Information

Details

MONOMER BY GEL FILTRATION CHROMATOGRAPHY/LIGHT SCATTERING AND BY NMR. T1/T2 (MS) = 792.1/78.18, TAUC = 9.7(NS) CONSISTENT WITH MOLECULAR WEIGHT. STRUCTURE DETERMINED BY TRIPLE RESONANCE NMR SPECTROSCOPY. NOESY ASSIGNMENTS BY CYANA2.1. 20 OF 100 STRUCTURES LOWEST TARGET FUNCTION SELECTED WITH CYANA2.1. SELECTED MODELS ARE FURTHER REFINED USING CNS IN EXPLICIT WATER SHELL (NILGES PROTOCOL WITH PARAM19). ASSIGNMENT STATS AROMATIC (SC) 92.6%, VL METHYL STEREOSPECIFIC 100%, UNAMBIGUOS SIDECHAIN NH2 100%. STRUCTURE BASED ON 1088 NOE, 166 DIHE. MAX NOE VIOLATION: 0.25 A (1MODEL); MAX DIHE VIOLATION: 3.2 DEG. 2 TOTAL CLOSE CONTACTS PER 20 MODELS. STRUCTURE QUALITY FACTOR > 1.8. SECONDARY STRUCTURE - BETA STRANDS: (8-17, 20-26, 29- 33, 51-60, 65-70). RMSD 0.4 BACKBONE, 0.8 ALL HEAVY ATOMS. MOLPROBITY CLASH: 16.80/-1.36 (RAW/Z). RPF SCORES ALL ASSIGNED PRECISION: 0.89, F-MEASURE: 0.93, DP-SCORE: 0.83.

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	refinement	CNS	1.1	BRUNGER, ADAMS, CLORE, GROS, NILGES
2	structure solution	CYANA	2.1
3	structure solution	NMRPipe
4	structure solution	AutoAssign
5	structure solution	Sparky	3.113
6	structure solution	TopSpin	2.1
7	structure solution	RPF(AUTOSTRUCTURE)	2.2.1
8	structure solution	PSVS	1.3
9	structure solution	MOLMOL
10	structure solution	PROCHECK
11	structure solution	MolProbity
12	structure solution	TALOS

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.

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2K52

Structure of uncharacterized protein MJ1198 from Methanocaldococcus jannaschii. Northeast Structural Genomics Target MjR117B