2KGO

Solution NMR structure of Zn finger protein YBIL from Escherichia coli. NESG target ET107, OCSP target EC0402

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-15N HSQC	0.7-1 mM [U-100% 13C; U-100% 15N] protein YBIL-1, 10 uM Zn sulfate-2, 10 mM [U-2H] DTT-3, 10 mM [U-2H] TRIS-4, 300 mM sodium chloride-5, 0.01 % sodium azide-6, 1 mM benzamidine-7, 1 mM Roche inhibitor-8	90% H2O/10% D2O	0.300	7.0	ambient	298
2	2D 1H-13C HSQC	0.7-1 mM [U-100% 13C; U-100% 15N] protein YBIL-1, 10 uM Zn sulfate-2, 10 mM [U-2H] DTT-3, 10 mM [U-2H] TRIS-4, 300 mM sodium chloride-5, 0.01 % sodium azide-6, 1 mM benzamidine-7, 1 mM Roche inhibitor-8	90% H2O/10% D2O	0.300	7.0	ambient	298
3	2D 1H-13C CT-HSQC	0.7-1 mM [U-100% 13C; U-100% 15N] protein YBIL-1, 10 uM Zn sulfate-2, 10 mM [U-2H] DTT-3, 10 mM [U-2H] TRIS-4, 300 mM sodium chloride-5, 0.01 % sodium azide-6, 1 mM benzamidine-7, 1 mM Roche inhibitor-8	90% H2O/10% D2O	0.300	7.0	ambient	298
4	3D CBCA(CO)NH	0.7-1 mM [U-100% 13C; U-100% 15N] protein YBIL-1, 10 uM Zn sulfate-2, 10 mM [U-2H] DTT-3, 10 mM [U-2H] TRIS-4, 300 mM sodium chloride-5, 0.01 % sodium azide-6, 1 mM benzamidine-7, 1 mM Roche inhibitor-8	90% H2O/10% D2O	0.300	7.0	ambient	298
5	3D HNCO	0.7-1 mM [U-100% 13C; U-100% 15N] protein YBIL-1, 10 uM Zn sulfate-2, 10 mM [U-2H] DTT-3, 10 mM [U-2H] TRIS-4, 300 mM sodium chloride-5, 0.01 % sodium azide-6, 1 mM benzamidine-7, 1 mM Roche inhibitor-8	90% H2O/10% D2O	0.300	7.0	ambient	298
6	3D HNCA	0.7-1 mM [U-100% 13C; U-100% 15N] protein YBIL-1, 10 uM Zn sulfate-2, 10 mM [U-2H] DTT-3, 10 mM [U-2H] TRIS-4, 300 mM sodium chloride-5, 0.01 % sodium azide-6, 1 mM benzamidine-7, 1 mM Roche inhibitor-8	90% H2O/10% D2O	0.300	7.0	ambient	298
7	3D C(CO)NH TOCSY	0.7-1 mM [U-100% 13C; U-100% 15N] protein YBIL-1, 10 uM Zn sulfate-2, 10 mM [U-2H] DTT-3, 10 mM [U-2H] TRIS-4, 300 mM sodium chloride-5, 0.01 % sodium azide-6, 1 mM benzamidine-7, 1 mM Roche inhibitor-8	90% H2O/10% D2O	0.300	7.0	ambient	298
8	3D HBHA(CO)NH	0.7-1 mM [U-100% 13C; U-100% 15N] protein YBIL-1, 10 uM Zn sulfate-2, 10 mM [U-2H] DTT-3, 10 mM [U-2H] TRIS-4, 300 mM sodium chloride-5, 0.01 % sodium azide-6, 1 mM benzamidine-7, 1 mM Roche inhibitor-8	90% H2O/10% D2O	0.300	7.0	ambient	298
9	3D H(CCO)NH TOCSY	0.7-1 mM [U-100% 13C; U-100% 15N] protein YBIL-1, 10 uM Zn sulfate-2, 10 mM [U-2H] DTT-3, 10 mM [U-2H] TRIS-4, 300 mM sodium chloride-5, 0.01 % sodium azide-6, 1 mM benzamidine-7, 1 mM Roche inhibitor-8	90% H2O/10% D2O	0.300	7.0	ambient	298
10	3D H(C)CH-TOCSY aliphatic	0.7-1 mM [U-100% 13C; U-100% 15N] protein YBIL-1, 10 uM Zn sulfate-2, 10 mM [U-2H] DTT-3, 10 mM [U-2H] TRIS-4, 300 mM sodium chloride-5, 0.01 % sodium azide-6, 1 mM benzamidine-7, 1 mM Roche inhibitor-8	90% H2O/10% D2O	0.300	7.0	ambient	298
11	3D (H)CCH-TOCSY aliphatic	0.7-1 mM [U-100% 13C; U-100% 15N] protein YBIL-1, 10 uM Zn sulfate-2, 10 mM [U-2H] DTT-3, 10 mM [U-2H] TRIS-4, 300 mM sodium chloride-5, 0.01 % sodium azide-6, 1 mM benzamidine-7, 1 mM Roche inhibitor-8	90% H2O/10% D2O	0.300	7.0	ambient	298
12	3D 15N-NOESY-HSQC	0.7-1 mM [U-100% 13C; U-100% 15N] protein YBIL-1, 10 uM Zn sulfate-2, 10 mM [U-2H] DTT-3, 10 mM [U-2H] TRIS-4, 300 mM sodium chloride-5, 0.01 % sodium azide-6, 1 mM benzamidine-7, 1 mM Roche inhibitor-8	90% H2O/10% D2O	0.300	7.0	ambient	298
13	3D 13C-NOESY-HSQC aliphatic	0.7-1 mM [U-100% 13C; U-100% 15N] protein YBIL-1, 10 uM Zn sulfate-2, 10 mM [U-2H] DTT-3, 10 mM [U-2H] TRIS-4, 300 mM sodium chloride-5, 0.01 % sodium azide-6, 1 mM benzamidine-7, 1 mM Roche inhibitor-8	90% H2O/10% D2O	0.300	7.0	ambient	298
14	3D 13C-NOESY-HSQC aromatic	0.7-1 mM [U-100% 13C; U-100% 15N] protein YBIL-1, 10 uM Zn sulfate-2, 10 mM [U-2H] DTT-3, 10 mM [U-2H] TRIS-4, 300 mM sodium chloride-5, 0.01 % sodium azide-6, 1 mM benzamidine-7, 1 mM Roche inhibitor-8	90% H2O/10% D2O	0.300	7.0	ambient	298
15	3D H(C)CH-TOCSY aromatic	0.7-1 mM [U-100% 13C; U-100% 15N] protein YBIL-1, 10 uM Zn sulfate-2, 10 mM [U-2H] DTT-3, 10 mM [U-2H] TRIS-4, 300 mM sodium chloride-5, 0.01 % sodium azide-6, 1 mM benzamidine-7, 1 mM Roche inhibitor-8	90% H2O/10% D2O	0.300	7.0	ambient	298
16	2D 1H-15N HSQC long range	0.7-1 mM [U-100% 13C; U-100% 15N] protein YBIL-1, 10 uM Zn sulfate-2, 10 mM [U-2H] DTT-3, 10 mM [U-2H] TRIS-4, 300 mM sodium chloride-5, 0.01 % sodium azide-6, 1 mM benzamidine-7, 1 mM Roche inhibitor-8	90% H2O/10% D2O	0.300	7.0	ambient	298
17	2D HBCBCGCDHD	0.7-1 mM [U-100% 13C; U-100% 15N] protein YBIL-1, 10 uM Zn sulfate-2, 10 mM [U-2H] DTT-3, 10 mM [U-2H] TRIS-4, 300 mM sodium chloride-5, 0.01 % sodium azide-6, 1 mM benzamidine-7, 1 mM Roche inhibitor-8	90% H2O/10% D2O	0.300	7.0	ambient	298
18	2D HBCBCGCDCEHE	0.7-1 mM [U-100% 13C; U-100% 15N] protein YBIL-1, 10 uM Zn sulfate-2, 10 mM [U-2H] DTT-3, 10 mM [U-2H] TRIS-4, 300 mM sodium chloride-5, 0.01 % sodium azide-6, 1 mM benzamidine-7, 1 mM Roche inhibitor-8	90% H2O/10% D2O	0.300	7.0	ambient	298

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

NMR Refinement
Method	Details	Software
molecular dynamics	water bath	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 (lowest energy)

Additional NMR Experimental Information
Details	1. THE 3 NOESY AND 3 HCCH-TYPE TOCSY SPECTRA WERE COLLECTED WITH NON-UNIFORM (NON-LINEAR) SAMPLING AND PROCESSED WITH MDDNMR SOFTWARE. 2. RESIDUES 54-90 FORM A GLOBULAR ZN2+ BINDING MODULE. 3. RESIDUES 1-27, 48-53 AND 91-108 ARE DISORDERED, AS JUDGED BY LACK OF LONG- AND MEDIUM- RANGE NOES AND RANDOM COIL INDEX AND CHEMICAL SHIFT INDEX PREDICTIONS. 4. HELIX 2 (RESIDUES 37-47), WHILE NOT PART OF THE GLOBULAR DOMAIN, IS SUPPORTED BY BOTH NOE AND CHEMICAL SHIFT DATA (RANDOM COIL INDEX, CHEMICAL SHIFT INDEX, TALOS). 5. RESIDUES 28-36 (HELIX 1) APPEAR TO FORM A NASCENT HELIX WITH SOME MEDIUM RANGE NOES, BUT CHEMICAL SHIFT DATA (RANDOM COIL INDEX, CHEMICAL SHIFT INDEX) SUGGEST IT MAY NOT BE A STABLE HELIX.

Additional NMR Experimental Information

Details

1. THE 3 NOESY AND 3 HCCH-TYPE TOCSY SPECTRA WERE COLLECTED WITH NON-UNIFORM (NON-LINEAR) SAMPLING AND PROCESSED WITH MDDNMR SOFTWARE. 2. RESIDUES 54-90 FORM A GLOBULAR ZN2+ BINDING MODULE. 3. RESIDUES 1-27, 48-53 AND 91-108 ARE DISORDERED, AS JUDGED BY LACK OF LONG- AND MEDIUM- RANGE NOES AND RANDOM COIL INDEX AND CHEMICAL SHIFT INDEX PREDICTIONS. 4. HELIX 2 (RESIDUES 37-47), WHILE NOT PART OF THE GLOBULAR DOMAIN, IS SUPPORTED BY BOTH NOE AND CHEMICAL SHIFT DATA (RANDOM COIL INDEX, CHEMICAL SHIFT INDEX, TALOS). 5. RESIDUES 28-36 (HELIX 1) APPEAR TO FORM A NASCENT HELIX WITH SOME MEDIUM RANGE NOES, BUT CHEMICAL SHIFT DATA (RANDOM COIL INDEX, CHEMICAL SHIFT INDEX) SUGGEST IT MAY NOT BE A STABLE HELIX.

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	refinement	CNS		Brunger, Adams, Clore, Gros, Nilges and Read
2	structure solution	CYANA		Guntert, Mumenthaler and Wuthrich
3	chemical shift assignment	ABACUS		A. Lemak
4	data analysis	ABACUS		A. Lemak
5	geometry optimization	TALOS		Cornilescu, Delaglio and Bax
6	data analysis	Analysis	2.06	CCPN
7	peak picking	Analysis	2.06	CCPN
8	processing	NMRPipe		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
9	processing	MddNMR		V. Orekhov, I. Ibraghimov

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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2KGO

Solution NMR structure of Zn finger protein YBIL from Escherichia coli. NESG target ET107, OCSP target EC0402