2K3A | pdb_00002k3a

NMR solution structure of Staphylococcus saprophyticus CHAP (cysteine, histidine-dependent amidohydrolases/peptidases) domain protein. Northeast Structural Genomics Consortium target SyR11

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-15N HSQC	0.66 mM [U-100% 13C; U-100% 15N] protein, 20 mM MES, 100 mM DTT, 100 mM sodium chloride, 0.02 % sodium azide, 5 mM Calcium Chloride, 5 % D2O	95% H2O/5% D2O	0.1	6.5	ambient	298
2	2D 1H-13C HSQC	0.66 mM [U-100% 13C; U-100% 15N] protein, 20 mM MES, 100 mM DTT, 100 mM sodium chloride, 0.02 % sodium azide, 5 mM Calcium Chloride, 5 % D2O	95% H2O/5% D2O	0.1	6.5	ambient	298
3	3D 1H-15N NOESY	0.66 mM [U-100% 13C; U-100% 15N] protein, 20 mM MES, 100 mM DTT, 100 mM sodium chloride, 0.02 % sodium azide, 5 mM Calcium Chloride, 5 % D2O	95% H2O/5% D2O	0.1	6.5	ambient	298
4	3D 1H-13C NOESY	0.66 mM [U-100% 13C; U-100% 15N] protein, 20 mM MES, 100 mM DTT, 100 mM sodium chloride, 0.02 % sodium azide, 5 mM Calcium Chloride, 5 % D2O	95% H2O/5% D2O	0.1	6.5	ambient	298
5	3D HNCACB	0.66 mM [U-100% 13C; U-100% 15N] protein, 20 mM MES, 100 mM DTT, 100 mM sodium chloride, 0.02 % sodium azide, 5 mM Calcium Chloride, 5 % D2O	95% H2O/5% D2O	0.1	6.5	ambient	298
6	3D HNCA	0.66 mM [U-100% 13C; U-100% 15N] protein, 20 mM MES, 100 mM DTT, 100 mM sodium chloride, 0.02 % sodium azide, 5 mM Calcium Chloride, 5 % D2O	95% H2O/5% D2O	0.1	6.5	ambient	298
7	3D HNCO	0.66 mM [U-100% 13C; U-100% 15N] protein, 20 mM MES, 100 mM DTT, 100 mM sodium chloride, 0.02 % sodium azide, 5 mM Calcium Chloride, 5 % D2O	95% H2O/5% D2O	0.1	6.5	ambient	298
8	3D HBHA(CO)NH	0.66 mM [U-100% 13C; U-100% 15N] protein, 20 mM MES, 100 mM DTT, 100 mM sodium chloride, 0.02 % sodium azide, 5 mM Calcium Chloride, 5 % D2O	95% H2O/5% D2O	0.1	6.5	ambient	298
9	3D HCCH-TOCSY	0.66 mM [U-100% 13C; U-100% 15N] protein, 20 mM MES, 100 mM DTT, 100 mM sodium chloride, 0.02 % sodium azide, 5 mM Calcium Chloride, 5 % D2O	95% H2O/5% D2O	0.1	6.5	ambient	298
10	3D HCCH-COSY	0.66 mM [U-100% 13C; U-100% 15N] protein, 20 mM MES, 100 mM DTT, 100 mM sodium chloride, 0.02 % sodium azide, 5 mM Calcium Chloride, 5 % D2O	95% H2O/5% D2O	0.1	6.5	ambient	298
11	3D CCH-TOCSY	0.66 mM [U-100% 13C; U-100% 15N] protein, 20 mM MES, 100 mM DTT, 100 mM sodium chloride, 0.02 % sodium azide, 5 mM Calcium Chloride, 5 % D2O	95% H2O/5% D2O	0.1	6.5	ambient	298
12	3D HN(COCA)CB	0.66 mM [U-100% 13C; U-100% 15N] protein, 20 mM MES, 100 mM DTT, 100 mM sodium chloride, 0.02 % sodium azide, 5 mM Calcium Chloride, 5 % D2O	95% H2O/5% D2O	0.1	6.5	ambient	298
13	3D HNCACO	0.66 mM [U-100% 13C; U-100% 15N] protein, 20 mM MES, 100 mM DTT, 100 mM sodium chloride, 0.02 % sodium azide, 5 mM Calcium Chloride, 5 % D2O	95% H2O/5% D2O	0.1	6.5	ambient	298
14	2D 1H-13C HSQC	0.96 mM [5% 13C; U-100% 15N] protein, 20 mM MES, 100 mM DTT, 100 mM sodium chloride, 0.02 % sodium azide, 5 mM Calcium Chloride, 5 % D2O	95% H2O/5% D2O	0.1	6.5	ambient	298
15	T1/T2 relaxation	0.96 mM [5% 13C; U-100% 15N] protein, 20 mM MES, 100 mM DTT, 100 mM sodium chloride, 0.02 % sodium azide, 5 mM Calcium Chloride, 5 % D2O	95% H2O/5% D2O	0.1	6.5	ambient	298
16	N15 Het-NOE	0.96 mM [5% 13C; U-100% 15N] protein, 20 mM MES, 100 mM DTT, 100 mM sodium chloride, 0.02 % sodium azide, 5 mM Calcium Chloride, 5 % D2O	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
molecular dynamics	STRUCTURE DETERMINED BY TRIPLE RESONANCE NMR SPECTROSCOPY. NOESY ASSIGNMENTS MADE WITH ITERATIVE METHOD USING CYANA-2.1 FOR SIMULATED ANNEALING AND AUTOSTRUCTURE 2.1. LOWEST TARGET FUNCTION SELECTED. CONVERGED STRUCTURES ARE FURTHER REFINED USING CNS IN EXPLICIT WATER SHELL (NIELGES PROTOCOL WITH PARAM19). MONOMER UNDER NMR CONDITIONS. TC = 7.0 +/- 0.1 NS (1D T1/T2). ASSIGNMENT STATS (EXCLUDING C-TERM TAG): BACKBONE 98.1%, SIDECHAIN 92.0%, AROMATIC (SC) 92.45%, VL METHYL STEREOSPECIFIC 88.23%, UNAMBIGUOS SIDECHAIN NH2 100%. STRUCTURE BASED ON 1111 NOE, 70 H-BOND, 124 DIHEDRAL. 100 STRUCTURES CALCULATED 20 LOWEST ENERGY SUBMITTED. MAX NOE VIOLATION 0.34 A (1MODEL), MAX DIHEDRAL 3.60 DEG. STRUCTURE QUALITY FACTOR PSVS 1.3: ORDERED RESIDUES RANGES - ALPHA HELIX (57-64, 76-86, 143-146), B-STRAND (89-91, 150-153, 98-101, 110-116, 122-127, 136-141) [S(PHI)+S(PSI)] > 1.8. RMSD 0.5 BB, 0.8 ALL HEAVY ATOMS. RAMA: 92.4% MOST FAV, 7.6% ADDTL. ALL., 0.0 GEN. ALL., 0.0% DISALL. PROCHECK (PSI-PHI): -0.30/-0.87 (RAW/Z), PROCHECK (ALL): -0.20/-1.18 (RAW/Z), MOLPROBITY CLASH: 11.42/-0.43 (RAW/Z) . RPF SCORES ALL ASSIGNED RESIDUES (FIT OF NOESY PEAKLISTS TO STRUCTURE): RECALL: 0.925, PRECISION: 0.884, F-MEASURE: 0.904, DP-SCORE: 0.763.	TopSpin

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

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	data acquisition	TopSpin	1.3	Bruker Biospin
2	processing	NMRPipe		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
3	data analysis	Sparky	3.113	Goddard
4	chemical shift assignment	AutoAssign	2.0	Zimmerman, Moseley, Kulikowski and Montelione
5	structure solution	AutoStructure	2.1.1	Huang, Tejero, Powers and Montelione
6	structure solution	CYANA	2.1	Guntert, Mumenthaler and Wuthrich
7	refinement	X-PLOR NIH	2.11.2	Schwieters, Kuszewski, Tjandra and Clore
8	refinement	CNS	1.1	Brunger, Adams, Clore, Gros, Nilges and Read
9	visualization	MOLMOL	2k2	Koradi, Billeter and Wuthrich
10	validation	PSVS	1.3	Bhattacharya and Montelione
11	validation	Procheck		Laskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Tho
12	validation	PROSA		Sippl
13	validation	PdbStat		Tejero R.; Montelione GT
14	validation	MolProbity		Richardson
15	validation	VERIFY3D		Luethy et. al.