2MIQ | pdb_00002miq

Solution NMR Structure of PHD Type 1 Zinc Finger Domain 1 of Lysine-specific Demethylase Lid from Drosophila melanogaster, Northeast Structural Genomics Consortium (NESG) Target FR824J

SOLUTION NMR

---

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-15N HSQC	0.321 mM 13C and 15N labeled protein	90% H2O/10% D2O		6.5	ambient	298
2	3D HNCO	0.321 mM 13C and 15N labeled protein	90% H2O/10% D2O		6.5	ambient	298
3	3D CBCA(CO)NH	0.321 mM 13C and 15N labeled protein	90% H2O/10% D2O		6.5	ambient	298
4	3D HNCACB	0.321 mM 13C and 15N labeled protein	90% H2O/10% D2O		6.5	ambient	298
5	3D HBHA(CO)NH	0.321 mM 13C and 15N labeled protein	90% H2O/10% D2O		6.5	ambient	298
6	3D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY	0.321 mM 13C and 15N labeled protein	90% H2O/10% D2O		6.5	ambient	298
7	2D 1H-13C ct HSQC aliphatic	0.321 mM 13C and 15N labeled protein	90% H2O/10% D2O		6.5	ambient	298
8	2D 1H-13C ct HSQC aromatic	0.321 mM 13C and 15N labeled protein	90% H2O/10% D2O		6.5	ambient	298
9	3D HN(CA)CO	0.321 mM 13C and 15N labeled protein	90% H2O/10% D2O		6.5	ambient	298
10	3D (H)CCH-COSY-ali	0.321 mM 13C and 15N labeled protein	90% H2O/10% D2O		6.5	ambient	298
11	3D (H)CCH-COSY aro	0.321 mM 13C and 15N labeled protein	90% H2O/10% D2O		6.5	ambient	298
12	3D (H)CCH-TOCSY ali	0.321 mM 13C and 15N labeled protein	90% H2O/10% D2O		6.5	ambient	298
13	2D gNfHSQC_His	0.321 mM 10% 13C and 100% 15N labeled protein	90% H2O/10% D2O		6.5	ambient	298
14	2D 1H-15N HSQC	0.321 mM 10% 13C and 100% 15N labeled protein	90% H2O/10% D2O		6.5	ambient	298
15	2D 1H-13C ct-HSQC(28ms)	0.321 mM 10% 13C and 100% 15N labeled protein	90% H2O/10% D2O		6.5	ambient	298
16	2D 1H-13C ct- HSQC(42ms)	0.321 mM 10% 13C and 100% 15N labeled protein	90% H2O/10% D2O		6.5	ambient	298
17	2D 1H-13C ct-HSQC(56ms)	0.321 mM 10% 13C and 100% 15N labeled protein	90% H2O/10% D2O		6.5	ambient	298
18	2D J-modulation 1H-15N HSQC	0.321 mM 10% 13C and 100% 15N labeled protein	90% H2O/10% D2O		6.5	ambient	298

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

NMR Refinement
Method	Details	Software
simulated annealing	Structure determination was performed by running CYANA and ASDP in parallel using NOE-based constraints and PHI and PSI dihedral angle constraints from TALOS+. Consensus peak assignments were selected and used in iterative refinement with CYANA. The 20 conformers out of 100 with the lowest target function were further refined by simulated annealing in explicit water bath using the program CNS with PARAM19 force field NMR Ensemble Information	CNS

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	refinement	CNS		Brunger, Adams, Clore, Gros, Nilges and Read
2	structure solution	CNS		Brunger, Adams, Clore, Gros, Nilges and Read
3	geometry optimization	CNS		Brunger, Adams, Clore, Gros, Nilges and Read
4	processing	CNS		Brunger, Adams, Clore, Gros, Nilges and Read
5	data analysis	CNS		Brunger, Adams, Clore, Gros, Nilges and Read
6	refinement	PROSA		Guntert
7	structure solution	PROSA		Guntert
8	geometry optimization	PROSA		Guntert
9	processing	PROSA		Guntert
10	data analysis	PROSA		Guntert
11	refinement	CARA		Keller and Wuthrich
12	structure solution	CARA		Keller and Wuthrich
13	geometry optimization	CARA		Keller and Wuthrich
14	processing	CARA		Keller and Wuthrich
15	data analysis	CARA		Keller and Wuthrich
16	refinement	CSI		David Wishart,Leigh Willard,Tim Jellard,Brian Sykes
17	sstructure solution	CSI		David Wishart,Leigh Willard,Tim Jellard,Brian Sykes
18	geometry optimization	CSI		David Wishart,Leigh Willard,Tim Jellard,Brian Sykes
19	processing	CSI		David Wishart,Leigh Willard,Tim Jellard,Brian Sykes
20	data analysis	CSI		David Wishart,Leigh Willard,Tim Jellard,Brian Sykes
21	refinement	CYANA	3.0	Guntert, Mumenthaler and Wuthrich
22	geometry optimization	CYANA	3.0	Guntert, Mumenthaler and Wuthrich
23	structure solution	CYANA	3.0	Guntert, Mumenthaler and Wuthrich
24	data analysis	AutoStructure	2.1	Huang, Tejero, Powers and Montelione
25	refinement	AutoStructure	2.1	Huang, Tejero, Powers and Montelione
26	data analysis	AutoAssign	2.1	Zimmerman, Moseley, Kulikowski and Montelione
27	chemical shift assignment	AutoAssign	2.1	Zimmerman, Moseley, Kulikowski and Montelione
28	data analysis	XEASY		Bartels et al.
29	collection	VnmrJ		Varian
30	geometry optimization	TALOS+		Shen, Cornilescu, Delaglio and Bax
31	structure validation	PSVS		Bhattacharya, Montelione
32	data analysis	MOLMOL		Koradi, Billeter and Wuthrich