2K5V

SOLUTION NMR STRUCTURE OF the second OB-fold domain of replication protein A from Methanococcus maripaludis. NORTHEAST STRUCTURAL GENOMICS TARGET MrR110B.

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-15N HSQC	1.18 MM [U-100% 13C 15N] MRR110B, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 95% H2O/ 5% D2O; 1.18 MM [U-100% 13C; U -100% 15N] MRR110B, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 100% D2O; 0.94 MM [U-5% 13C; U-100% 15N] MRR110B, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 95% H2O/5% D2O		0.1	6.5	AMBIENT	298
2	2D 1H-13C HSQC	1.18 MM [U-100% 13C 15N] MRR110B, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 95% H2O/ 5% D2O; 1.18 MM [U-100% 13C; U -100% 15N] MRR110B, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 100% D2O; 0.94 MM [U-5% 13C; U-100% 15N] MRR110B, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 95% H2O/5% D2O		0.1	6.5	AMBIENT	298
3	3D HNCO	1.18 MM [U-100% 13C 15N] MRR110B, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 95% H2O/ 5% D2O; 1.18 MM [U-100% 13C; U -100% 15N] MRR110B, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 100% D2O; 0.94 MM [U-5% 13C; U-100% 15N] MRR110B, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 95% H2O/5% D2O		0.1	6.5	AMBIENT	298
4	3D HN(CA)CO	1.18 MM [U-100% 13C 15N] MRR110B, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 95% H2O/ 5% D2O; 1.18 MM [U-100% 13C; U -100% 15N] MRR110B, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 100% D2O; 0.94 MM [U-5% 13C; U-100% 15N] MRR110B, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 95% H2O/5% D2O		0.1	6.5	AMBIENT	298
5	3D CBCA(CO)NH	1.18 MM [U-100% 13C 15N] MRR110B, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 95% H2O/ 5% D2O; 1.18 MM [U-100% 13C; U -100% 15N] MRR110B, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 100% D2O; 0.94 MM [U-5% 13C; U-100% 15N] MRR110B, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 95% H2O/5% D2O		0.1	6.5	AMBIENT	298
6	3D HNCACB	1.18 MM [U-100% 13C 15N] MRR110B, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 95% H2O/ 5% D2O; 1.18 MM [U-100% 13C; U -100% 15N] MRR110B, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 100% D2O; 0.94 MM [U-5% 13C; U-100% 15N] MRR110B, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 95% H2O/5% D2O		0.1	6.5	AMBIENT	298
7	3D HBHA(CO)NH	1.18 MM [U-100% 13C 15N] MRR110B, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 95% H2O/ 5% D2O; 1.18 MM [U-100% 13C; U -100% 15N] MRR110B, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 100% D2O; 0.94 MM [U-5% 13C; U-100% 15N] MRR110B, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 95% H2O/5% D2O		0.1	6.5	AMBIENT	298
8	3D HCCH-COSY ALIPHATIC	1.18 MM [U-100% 13C 15N] MRR110B, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 95% H2O/ 5% D2O; 1.18 MM [U-100% 13C; U -100% 15N] MRR110B, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 100% D2O; 0.94 MM [U-5% 13C; U-100% 15N] MRR110B, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 95% H2O/5% D2O		0.1	6.5	AMBIENT	298
9	3D HCCH-TOCSY ALIPHATIC	1.18 MM [U-100% 13C 15N] MRR110B, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 95% H2O/ 5% D2O; 1.18 MM [U-100% 13C; U -100% 15N] MRR110B, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 100% D2O; 0.94 MM [U-5% 13C; U-100% 15N] MRR110B, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 95% H2O/5% D2O		0.1	6.5	AMBIENT	298
10	3D CCH-TOCSY ALIPHATIC	1.18 MM [U-100% 13C 15N] MRR110B, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 95% H2O/ 5% D2O; 1.18 MM [U-100% 13C; U -100% 15N] MRR110B, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 100% D2O; 0.94 MM [U-5% 13C; U-100% 15N] MRR110B, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 95% H2O/5% D2O		0.1	6.5	AMBIENT	298
11	3D HNHA	1.18 MM [U-100% 13C 15N] MRR110B, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 95% H2O/ 5% D2O; 1.18 MM [U-100% 13C; U -100% 15N] MRR110B, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 100% D2O; 0.94 MM [U-5% 13C; U-100% 15N] MRR110B, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 95% H2O/5% D2O		0.1	6.5	AMBIENT	298
12	3D SIMULTANEOUS CN NOESY	1.18 MM [U-100% 13C 15N] MRR110B, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 95% H2O/ 5% D2O; 1.18 MM [U-100% 13C; U -100% 15N] MRR110B, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 100% D2O; 0.94 MM [U-5% 13C; U-100% 15N] MRR110B, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 95% H2O/5% D2O		0.1	6.5	AMBIENT	298
13	3D 1H-13C NOESY aromatic	1.18 MM [U-100% 13C 15N] MRR110B, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 95% H2O/ 5% D2O; 1.18 MM [U-100% 13C; U -100% 15N] MRR110B, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 100% D2O; 0.94 MM [U-5% 13C; U-100% 15N] MRR110B, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 95% H2O/5% D2O		0.1	6.5	AMBIENT	298
14	2D 1H-13C HSQC HIGH RES. (L/V STEREOASSIGNMENT)	1.18 MM [U-100% 13C 15N] MRR110B, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 95% H2O/ 5% D2O; 1.18 MM [U-100% 13C; U -100% 15N] MRR110B, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 100% D2O; 0.94 MM [U-5% 13C; U-100% 15N] MRR110B, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 95% H2O/5% D2O		0.1	6.5	AMBIENT	298
15	2D 1H-15N HETNOE	1.18 MM [U-100% 13C 15N] MRR110B, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 95% H2O/ 5% D2O; 1.18 MM [U-100% 13C; U -100% 15N] MRR110B, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 100% D2O; 0.94 MM [U-5% 13C; U-100% 15N] MRR110B, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 95% H2O/5% D2O		0.1	6.5	AMBIENT	298
16	2D 1H-15N T1/T2	1.18 MM [U-100% 13C 15N] MRR110B, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 95% H2O/ 5% D2O; 1.18 MM [U-100% 13C; U -100% 15N] MRR110B, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 100% D2O; 0.94 MM [U-5% 13C; U-100% 15N] MRR110B, 20 MM MES, 100 MM SODIUM CHLORIDE, 5 MM CALCIUM CHLORIDE, 10 MM DTT, 0.02 % SODIUM AZIDE, 95% H2O/5% D2O		0.1	6.5	AMBIENT	298

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

NMR Refinement
Method	Details	Software
simulated annealing	THE FINAL STRUCTURES ARE BASED ON A TOTAL OF 1692 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS AND 125 DIHEDRAL ANGLE CONSTRAINTS; 0 HYDROGEN BOND CONSTRAINTS (18.5 CONSTRAINTS PER RESIDUE, 6.2 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 172 TO 269 BY PSVS 1.3). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING CYANA 2.1. 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 THE SIDE CHAIN ASSIGNMENTS WERE COMPLETED MANUALLY. AUTOMATIC NOESY ASSIGNMENTS WERE DETERMINED USING CYANA 2.1. 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, 100%, SIDE CHAIN, 99.7%, AROMATICS, 100%, STEREOSPECIFIC METHYL, 100%, STEREOSPECIFIC SIDE CHAIN NH2: 100%. FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUES 172 TO 269, PSVS 1.3), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE: 173-204,209-249,254-265: (A) RMSD (ORDERED RESIDUES): BB, 0.6, HEAVY ATOM, 1.0. (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 92.4%, ADDITIONALLY ALLOWED, 6.6%, GENEROUSLY ALLOWED, 1.0%, DISALLOWED, 0.0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, -0.60/-2.05, ALL, -0.36/-2.13. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 16.29/-1.27 (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (RESIDUES 172-269): RECALL, 0.990, PRECISION, 0.933, F-MEASURE, 0.961, DP-SCORE, 0.836. (F) NUMBER OF CLOSE CONTACTS PER 20 MODELS: 2. 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]: 172,205-208,250-253, 266-269.

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 THE SIDE CHAIN ASSIGNMENTS WERE COMPLETED MANUALLY. AUTOMATIC NOESY ASSIGNMENTS WERE DETERMINED USING CYANA 2.1. 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, 100%, SIDE CHAIN, 99.7%, AROMATICS, 100%, STEREOSPECIFIC METHYL, 100%, STEREOSPECIFIC SIDE CHAIN NH2: 100%. FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUES 172 TO 269, PSVS 1.3), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE: 173-204,209-249,254-265: (A) RMSD (ORDERED RESIDUES): BB, 0.6, HEAVY ATOM, 1.0. (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 92.4%, ADDITIONALLY ALLOWED, 6.6%, GENEROUSLY ALLOWED, 1.0%, DISALLOWED, 0.0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, -0.60/-2.05, ALL, -0.36/-2.13. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 16.29/-1.27 (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (RESIDUES 172-269): RECALL, 0.990, PRECISION, 0.933, F-MEASURE, 0.961, DP-SCORE, 0.836. (F) NUMBER OF CLOSE CONTACTS PER 20 MODELS: 2. 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]: 172,205-208,250-253, 266-269.

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	refinement	CNS	1.2	BRUNGER, ADAMS, CLORE, GROS, NILGES
2	structure solution	TopSpin	2.1
3	structure solution	AutoAssign	2.4.0
4	structure solution	NMRPipe	2.3
5	structure solution	CYANA	2.1
6	structure solution	CNS	1.2
7	structure solution	Sparky	3.113
8	structure solution	AutoStructure	2.2.1
9	structure solution	PSVS	1.3
10	structure solution	PdbStat	5.0

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 R01GM133198.

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2K5V

SOLUTION NMR STRUCTURE OF the second OB-fold domain of replication protein A from Methanococcus maripaludis. NORTHEAST STRUCTURAL GENOMICS TARGET MrR110B.