2KYW

Solution NMR Structure of a domain of adhesion exoprotein from Pediococcus pentosaceus, Northeast Structural Genomics Consortium Target PtR41O

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-15N HSQC	1.0 mM [U-100% 13C; U-100% 15N] PtR41O-1, 100 mM sodium chloride-2, 5 mM calcium chloride-3, 10 mM DTT-4, 20 mM MES-5, 0.02 % NaN3-6, 50 uM DSS-7	90% H2O/10% D2O	117.5	6.5	ambient	298
2	2D 1H-13C CT-HSQC ali	1.0 mM [U-100% 13C; U-100% 15N] PtR41O-1, 100 mM sodium chloride-2, 5 mM calcium chloride-3, 10 mM DTT-4, 20 mM MES-5, 0.02 % NaN3-6, 50 uM DSS-7	90% H2O/10% D2O	117.5	6.5	ambient	298
3	2D 1H-13C CT-HSQC aro	1.0 mM [U-100% 13C; U-100% 15N] PtR41O-1, 100 mM sodium chloride-2, 5 mM calcium chloride-3, 10 mM DTT-4, 20 mM MES-5, 0.02 % NaN3-6, 50 uM DSS-7	90% H2O/10% D2O	117.5	6.5	ambient	298
4	3D HNCO	1.0 mM [U-100% 13C; U-100% 15N] PtR41O-1, 100 mM sodium chloride-2, 5 mM calcium chloride-3, 10 mM DTT-4, 20 mM MES-5, 0.02 % NaN3-6, 50 uM DSS-7	90% H2O/10% D2O	117.5	6.5	ambient	298
5	3D HN(CA)CO	1.0 mM [U-100% 13C; U-100% 15N] PtR41O-1, 100 mM sodium chloride-2, 5 mM calcium chloride-3, 10 mM DTT-4, 20 mM MES-5, 0.02 % NaN3-6, 50 uM DSS-7	90% H2O/10% D2O	117.5	6.5	ambient	298
6	GFT CBCA(CO)NH	1.0 mM [U-100% 13C; U-100% 15N] PtR41O-1, 100 mM sodium chloride-2, 5 mM calcium chloride-3, 10 mM DTT-4, 20 mM MES-5, 0.02 % NaN3-6, 50 uM DSS-7	90% H2O/10% D2O	117.5	6.5	ambient	298
7	GFT HNCACB	1.0 mM [U-100% 13C; U-100% 15N] PtR41O-1, 100 mM sodium chloride-2, 5 mM calcium chloride-3, 10 mM DTT-4, 20 mM MES-5, 0.02 % NaN3-6, 50 uM DSS-7	90% H2O/10% D2O	117.5	6.5	ambient	298
8	3D HBHA(CO)NH	1.0 mM [U-100% 13C; U-100% 15N] PtR41O-1, 100 mM sodium chloride-2, 5 mM calcium chloride-3, 10 mM DTT-4, 20 mM MES-5, 0.02 % NaN3-6, 50 uM DSS-7	90% H2O/10% D2O	117.5	6.5	ambient	298
9	3D HCCH-TOCSY	1.0 mM [U-100% 13C; U-100% 15N] PtR41O-1, 100 mM sodium chloride-2, 5 mM calcium chloride-3, 10 mM DTT-4, 20 mM MES-5, 0.02 % NaN3-6, 50 uM DSS-7	90% H2O/10% D2O	117.5	6.5	ambient	298
10	3D HCCH-COSY ali	1.0 mM [U-100% 13C; U-100% 15N] PtR41O-1, 100 mM sodium chloride-2, 5 mM calcium chloride-3, 10 mM DTT-4, 20 mM MES-5, 0.02 % NaN3-6, 50 uM DSS-7	90% H2O/10% D2O	117.5	6.5	ambient	298
11	13C/15N-NOESY	1.0 mM [U-100% 13C; U-100% 15N] PtR41O-1, 100 mM sodium chloride-2, 5 mM calcium chloride-3, 10 mM DTT-4, 20 mM MES-5, 0.02 % NaN3-6, 50 uM DSS-7	90% H2O/10% D2O	117.5	6.5	ambient	298
12	2D 1H-13C CT-HSQC (methyl)	1.2 mM [U-5% 13C; U-100% 15N] PtR41O-8, 100 mM sodium chloride-9, 5 mM calcium chloride-10, 10 mM DTT-11, 20 mM MES-12, 0.02 % NaN3-13, 50 uM DSS-14	90% H2O/10% D2O	117.5	6.5	ambient	298
13	2D J-modulation 1H-15N HSQC	1.2 mM [U-5% 13C; U-100% 15N] PtR41O-8, 100 mM sodium chloride-9, 5 mM calcium chloride-10, 10 mM DTT-11, 20 mM MES-12, 0.02 % NaN3-13, 50 uM DSS-14	90% H2O/10% D2O	117.5	6.5	ambient	298
14	2D J-modulation 1H-15N HSQC	0.66 mM [U-5% 13C; U-100% 15N] PtR41O-15, 66 mM sodium chloride-16, 3.3 mM calcium chloride-17, 6.6 mM DTT-18, 13.2 mM MES-19, 0.0132 % NaN3-20, 33 uM DSS-21, 4 % poly ethylene glycol-22	83% H2O/17% D2O	117.5	6.5	ambient	298
15	2D J-modulation 1H-15N HSQC	0.66 mM [U-5% 13C; U-100% 15N] PtR41O-23, 66 mM sodium chloride-24, 3.3 mM calcium chloride-25, 6.6 mM DTT-26, 13.2 mM MES-27, 0.0132 % NaN3-28, 33 uM DSS-29, 13.25 mg/mL Pf1 phage-30	83% H2O/17% D2O	117.5	6.5	ambient	298

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

NMR Refinement
Method	Details	Software
simulated annealing	Structure determination was performed iteratively with CYANA v3.0 using NOE-based constraints, PHI and PSI dihedral angle constraints from TALOS+, and RDC constraints. 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	CNS

NMR Ensemble Information
Conformer Selection Criteria	target function
Conformers Calculated Total Number	100
Conformers Submitted Total Number	16
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	structure solution	CYANA	3.0	Guntert, Mumenthaler and Wuthrich
5	refinement	CYANA	3.0	Guntert, Mumenthaler and Wuthrich
6	structure solution	AutoStructure	2.2.1	Huang, Tejero, Powers and Montelione
7	chemical shift assignment	AutoAssign		Zimmerman, Moseley, Kulikowski and Montelione
8	processing	NMRPipe	2007.030.16.06	Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
9	data analysis	XEASY		Bartels et al.
10	collection	TopSpin		Bruker Biospin
11	collection	VnmrJ	2.1B	Varian
12	refinement	MOLMOL		Koradi, Billeter and Wuthrich
13	chemical shift assignment	CARA	1.8.4	Keller and Wuthrich
14	peak picking	CARA	1.8.4	Keller and Wuthrich
15	data analysis	CARA	1.8.4	Keller and Wuthrich
16	data analysis	TALOS+		Shen, Cornilescu, Delaglio and Bax
17	validation	PSVS	1.3	Bhattacharya and Montelione
18	data analysis	NMRDraw	3.0	Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
19	processing	PROSA		Guntert

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.

Prepare Data

Validate Data

Deposit Data

Help and Resources

2KYW

Solution NMR Structure of a domain of adhesion exoprotein from Pediococcus pentosaceus, Northeast Structural Genomics Consortium Target PtR41O