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BMRB: 18978

2M3X

Solution structure of Ph1500: a homohexameric protein centered on a 12-bladed beta-propeller

Authors

Varnay, I., Truffault, V., Kessler, H., Coles, M.

Assembly

Ph1500: a homohexameric protein centered on a 12-bladed beta-propeller

Entity

1. Ph1500 (polymer, Thiol state: not present), 147 monomers, 16705.53 × 6 Da Detail

EGVIMSELKL KPLPKVELPP DFVDVIRIKL QGKTVRTGDV IGISILGKEV KFKVVQAYPS PLRVEDRTKI TLVTHPVDVL EAKIKGIKDV ILDENLIVVI TEENEVLIFN QNLEELYRGK FENLNKVLVR NDLVVIIDEQ KLTLIRT

2. Ph1500N (polymer, Thiol state: not present), 83 monomers, 9429.060 Da Detail

MHHHHHHEGV IMSELKLKPL PKVELPPDFV DVIRIKLQGK TVRTGDVIGI SILGKEVKFK VVQAYPSPLR VEDRTKITLV THP

3. Ph1500C (polymer, Thiol state: not present), 78 monomers, 9202.545 Da Detail

MHHHHHHVDV LEAKIKGIKD VILDENLIVV ITEENEVLIF NQNLEELYRG KFENLNKVLV RNDLVVIIDE QKLTLIRT

Total weight

118864.78 Da

Max. entity weight

16705.53 Da

Source organism

Pyrococcus horikoshii

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 48.7 %, Completeness: 46.0 %, Completeness (bb): 46.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	46.0 % (1738 of 3780)	45.9 % (904 of 1970)	46.5 % (694 of 1494)	44.3 % (140 of 316)
Backbone	46.5 % (847 of 1820)	46.8 % (288 of 616)	46.4 % (422 of 910)	46.6 % (137 of 294)
Sidechain	45.8 % (1032 of 2254)	45.5 % (616 of 1354)	47.0 % (413 of 878)	13.6 % (3 of 22)
Aromatic	29.8 % (50 of 168)	29.8 % (25 of 84)	29.8 % (25 of 84)
Methyl	49.8 % (243 of 488)	49.6 % (121 of 244)	50.0 % (122 of 244)

1. Ph1500

EGVIMSELKL KPLPKVELPP DFVDVIRIKL QGKTVRTGDV IGISILGKEV KFKVVQAYPS PLRVEDRTKI TLVTHPVDVL EAKIKGIKDV ILDENLIVVI TEENEVLIFN QNLEELYRGK FENLNKVLVR NDLVVIIDEQ KLTLIRT

2. Ph1500N

MHHHHHHEGV IMSELKLKPL PKVELPPDFV DVIRIKLQGK TVRTGDVIGI SILGKEVKFK VVQAYPSPLR VEDRTKITLV THP

3. Ph1500C

MHHHHHHVDV LEAKIKGIKD VILDENLIVV ITEENEVLIF NQNLEELYRG KFENLNKVLV RNDLVVIIDE QKLTLIRT

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 353 K, pH 7.2

#	Name	Isotope labeling	Concentration
1	Ph1500C	[U-100% 13C; U-100% 15N]	1.2 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	250 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 353 K, pH 7.2

#	Name	Isotope labeling	Concentration
6	Ph1500C	[U-85% 2H; U-100% 13C; U-100% 15N]	0.6 mM
7	sodium phosphate	natural abundance	20 mM
8	sodium chloride	natural abundance	250 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 353 K, pH 7.2

#	Name	Isotope labeling	Concentration
11	Ph1500N	[U-100% 13C; U-100% 15N]	1.0 mM
12	sodium phosphate	natural abundance	50 mM
13	sodium chloride	natural abundance	50 mM
14	H2O	natural abundance	90 %
15	D2O	natural abundance	10 %

Sample #4

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 353 K, pH 7.2

#	Name	Isotope labeling	Concentration
16	Ph1500N	[U-100% 15N]	1.0 mM
17	sodium phosphate	natural abundance	20 mM
18	sodium chloride	natural abundance	50 mM
19	H2O	natural abundance	90 %
20	D2O	natural abundance	10 %

Sample #5

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 353 K, pH 7.2

#	Name	Isotope labeling	Concentration
21	Ph1500	[U-85% 2H; U-100% 13C; U-100% 15N]	0.6 mM
22	sodium phosphate	natural abundance	20 mM
23	sodium chloride	natural abundance	250 mM
24	H2O	natural abundance	90 %
25	D2O	natural abundance	10 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	2.6 ppm	internal	indirect	0.2514495
¹H	DSS	methyl protons	0.0 ppm	internal	direct	1.0
¹⁵N	DSS	methyl protons	0.0 ppm	internal	indirect	0.1013291

Referencing offset: 0.2 ppm, Outliers: 4 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	2.6 ppm	internal	indirect	0.2514495
¹H	DSS	methyl protons	0.0 ppm	internal	direct	1.0
¹⁵N	DSS	methyl protons	0.0 ppm	internal	indirect	0.1013291

Referencing offset: 0.2 ppm, Outliers: 4 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	2.6 ppm	internal	indirect	0.2514495
¹H	DSS	methyl protons	0.0 ppm	internal	direct	1.0
¹⁵N	DSS	methyl protons	0.0 ppm	internal	indirect	0.1013291

Referencing offset: -0.01 ppm, Outliers: 3 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	2.6 ppm	internal	indirect	0.2514495
¹H	DSS	methyl protons	0.0 ppm	internal	direct	1.0
¹⁵N	DSS	methyl protons	0.0 ppm	internal	indirect	0.1013291

Referencing offset: 1.35 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2M3X, Strand ID: A, B, C, D, E, F Detail

Release date

2013-02-17

Citation

Optimized measurement temperature gives access to the solution structure of a 49 kDa homohexameric β-propeller
Varnay, I., Truffault, V., Djuranovic, S., Ursinus, A., Coles, M., Kessler, H.
J. Am. Chem. Soc. (2010), 132, 15692-15698, PubMed 20961124 , DOI 10.1021/ja1064608 , Abstract

Related entities 2. Ph1500N, : 5 entities Detail

Related entities 3. Ph1500C, : 1 entities Detail

Experiments performed 31 experiments Detail

1 3D HNCO

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 7.0

#	Name	Isotope labeling	Concentration
11	Ph1500N	[U-100% 13C; U-100% 15N]	1.0 mM
12	sodium phosphate	natural abundance	50 mM
13	sodium chloride	natural abundance	50 mM
14	H2O	natural abundance	90 %
15	D2O	natural abundance	10 %

2 3D HNCACB

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 7.0

#	Name	Isotope labeling	Concentration
11	Ph1500N	[U-100% 13C; U-100% 15N]	1.0 mM
12	sodium phosphate	natural abundance	50 mM
13	sodium chloride	natural abundance	50 mM
14	H2O	natural abundance	90 %
15	D2O	natural abundance	10 %

3 3D CBCA(CO)NH

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 7.0

#	Name	Isotope labeling	Concentration
11	Ph1500N	[U-100% 13C; U-100% 15N]	1.0 mM
12	sodium phosphate	natural abundance	50 mM
13	sodium chloride	natural abundance	50 mM
14	H2O	natural abundance	90 %
15	D2O	natural abundance	10 %

4 3D HNHA

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 7.0

#	Name	Isotope labeling	Concentration
16	Ph1500N	[U-100% 15N]	1.0 mM
17	sodium phosphate	natural abundance	20 mM
18	sodium chloride	natural abundance	50 mM
19	H2O	natural abundance	90 %
20	D2O	natural abundance	10 %

5 3D HNHB

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 7.0

#	Name	Isotope labeling	Concentration
16	Ph1500N	[U-100% 15N]	1.0 mM
17	sodium phosphate	natural abundance	20 mM
18	sodium chloride	natural abundance	50 mM
19	H2O	natural abundance	90 %
20	D2O	natural abundance	10 %

6 3D 1H-15N NOESY

Instrument

Bruker DMX - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 7.0

#	Name	Isotope labeling	Concentration
16	Ph1500N	[U-100% 15N]	1.0 mM
17	sodium phosphate	natural abundance	20 mM
18	sodium chloride	natural abundance	50 mM
19	H2O	natural abundance	90 %
20	D2O	natural abundance	10 %

7 3D NNH-NOESY

Instrument

Bruker DMX - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 7.0

#	Name	Isotope labeling	Concentration
16	Ph1500N	[U-100% 15N]	1.0 mM
17	sodium phosphate	natural abundance	20 mM
18	sodium chloride	natural abundance	50 mM
19	H2O	natural abundance	90 %
20	D2O	natural abundance	10 %

8 3D CNH-NOESY

Instrument

Bruker DMX - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 7.0

#	Name	Isotope labeling	Concentration
11	Ph1500N	[U-100% 13C; U-100% 15N]	1.0 mM
12	sodium phosphate	natural abundance	50 mM
13	sodium chloride	natural abundance	50 mM
14	H2O	natural abundance	90 %
15	D2O	natural abundance	10 %

9 3D 1H-13C NOESY

Instrument

Bruker DMX - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 7.0

#	Name	Isotope labeling	Concentration
11	Ph1500N	[U-100% 13C; U-100% 15N]	1.0 mM
12	sodium phosphate	natural abundance	50 mM
13	sodium chloride	natural abundance	50 mM
14	H2O	natural abundance	90 %
15	D2O	natural abundance	10 %

10 3D CCH-NOESY

Instrument

Bruker DMX - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 7.0

#	Name	Isotope labeling	Concentration
11	Ph1500N	[U-100% 13C; U-100% 15N]	1.0 mM
12	sodium phosphate	natural abundance	50 mM
13	sodium chloride	natural abundance	50 mM
14	H2O	natural abundance	90 %
15	D2O	natural abundance	10 %

11 2D 15N-filtered 1H-1H NOESY

Instrument

Bruker DMX - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 K, pH 7.0

#	Name	Isotope labeling	Concentration
16	Ph1500N	[U-100% 15N]	1.0 mM
17	sodium phosphate	natural abundance	20 mM
18	sodium chloride	natural abundance	50 mM
19	H2O	natural abundance	90 %
20	D2O	natural abundance	10 %

12 3D trHNCO

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 7.2

#	Name	Isotope labeling	Concentration
6	Ph1500C	[U-85% 2H; U-100% 13C; U-100% 15N]	0.6 mM
7	sodium phosphate	natural abundance	20 mM
8	sodium chloride	natural abundance	250 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

13 3D trHN(CA)CO

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 7.2

#	Name	Isotope labeling	Concentration
6	Ph1500C	[U-85% 2H; U-100% 13C; U-100% 15N]	0.6 mM
7	sodium phosphate	natural abundance	20 mM
8	sodium chloride	natural abundance	250 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

14 3D trHNCA

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 7.2

#	Name	Isotope labeling	Concentration
6	Ph1500C	[U-85% 2H; U-100% 13C; U-100% 15N]	0.6 mM
7	sodium phosphate	natural abundance	20 mM
8	sodium chloride	natural abundance	250 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

15 3D trHNCACB

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 7.2

#	Name	Isotope labeling	Concentration
6	Ph1500C	[U-85% 2H; U-100% 13C; U-100% 15N]	0.6 mM
7	sodium phosphate	natural abundance	20 mM
8	sodium chloride	natural abundance	250 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

16 3D trHNCO