1YH5 | pdb_00001yh5

Solution NMR Structure of Protein yggU from Escherichia coli. Northeast Structural Genomics Consortium Target ER14.

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	3D 15N-NOESY	1.0 MM ER14 U-15N,13C IN 20MM MES, 50MM NACL, 5MM DTT, PH 6.5; 1.0 MM ER14 U-15N,13C IN 20MM MES, 50MM NACL, 5MM DTT, PH 6.5		50 mM NACL	6.5	AMBIENT	293
2	3D 13C-NOESY	1.0 MM ER14 U-15N,13C IN 20MM MES, 50MM NACL, 5MM DTT, PH 6.5; 1.0 MM ER14 U-15N,13C IN 20MM MES, 50MM NACL, 5MM DTT, PH 6.5		50 mM NACL	6.5	AMBIENT	293
3	3D AROMATIC 13C-NOESY	1.0 MM ER14 U-15N,13C IN 20MM MES, 50MM NACL, 5MM DTT, PH 6.5; 1.0 MM ER14 U-15N,13C IN 20MM MES, 50MM NACL, 5MM DTT, PH 6.5		50 mM NACL	6.5	AMBIENT	293
4	2D 15N	1.0 MM ER14 U-15N,13C IN 20MM MES, 50MM NACL, 5MM DTT, PH 6.5; 1.0 MM ER14 U-15N,13C IN 20MM MES, 50MM NACL, 5MM DTT, PH 6.5		50 mM NACL	6.5	AMBIENT	293
5	1H HSQC-J	1.0 MM ER14 U-15N,13C IN 20MM MES, 50MM NACL, 5MM DTT, PH 6.5; 1.0 MM ER14 U-15N,13C IN 20MM MES, 50MM NACL, 5MM DTT, PH 6.5		50 mM NACL	6.5	AMBIENT	293
6	2D 15N	1.0 MM ER14 U-15N,13C IN 20MM MES, 50MM NACL, 5MM DTT, PH 6.5; 1.0 MM ER14 U-15N,13C IN 20MM MES, 50MM NACL, 5MM DTT, PH 6.5		50 mM NACL	6.5	AMBIENT	293
7	1H MEXICO	1.0 MM ER14 U-15N,13C IN 20MM MES, 50MM NACL, 5MM DTT, PH 6.5; 1.0 MM ER14 U-15N,13C IN 20MM MES, 50MM NACL, 5MM DTT, PH 6.5		50 mM NACL	6.5	AMBIENT	293

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

NMR Refinement
Method	Details	Software
TORSION ANGLE DYNAMICS SIMULATED ANNEALING	THE STRUCTURE IS BASED ON A TOTAL OF 1031 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 207 DIHEDRAL ANGLE CONSTRAINTS, AND 56 HYDROGEN BOND CONSTRAINTS (12.6 CONSTRAINTS PER RESIDUE; 4.1 LONG-RANGE CONTRAINTS PER RESIDUE). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING AUTOSTRUCTURE WITH XPLOR.	X-PLOR 2.0.4 (NIH), AUTOSTRUCTURE

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	56
Conformers Submitted Total Number	10
Representative Model	1 (n/a)

Additional NMR Experimental Information

Details

THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY. AUTOMATIC BACKBONE RESONANCE ASSIGNMENTS WERE MADE USING AUTOASSIGN. AUTOMATIC NOESY ASSIGNMENTS AS WELL AS DISTANCE AND HYDROGEN BOND RESTRAINTS WERE DETERMINED USING THE AUTOSTRUCTURE PROGRAM. DIHEDRAL ANGLE RESTRAINTS WERE DETERMINED USING HYPER AND TALOS.FINAL STRUCTURE QUALITY FACTORS FOR THE ENSEMBLE, WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE 8-23,28-29,31-34,37-41,44-65,67-77,80-87: (A) RMSD FOR ORDERED RESIDUES: BB, 0.7 ANG; HEAVY ATOM, 1.2 ANG. (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED: 75.9%; ADDITIONALLY ALLOWED: 23.0%; GENEROUSLY ALLOWED, 1.0%; DISALLOWED, 0.2% (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z): BB, -1.14/-2.23; ALL, -1.0/-4.17. (D) MAGE MOLPROBITY CLASH SCORE (RAW/Z): 33.22/-4.18 (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA: F-MEASURE, 0.944; RECALL, 0.977; PRECISION, 0.802; DP-SCORE, 0.726.

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	refinement	X-PLOR 2.0.4 (NIH), AUTOSTRUCTURE	2.0.0	BRUNGER (X-PLOR), HUANG (AUTOSTRUCTURE)
2	structure solution	VNMR 6.1B	6.1B
3	structure solution	NMRPipe	2.1
4	structure solution	Sparky	3.106
5	structure solution	AutoAssign	1.9
6	structure solution	AutoStructure	2.0.0
7	structure solution	HYPER	2.70
8	structure solution	TALOS	2.1
9	structure solution	PdbStat	3.27
10	structure solution	XPLOR	2.0.4 (NIH), PSVS 1.0