BMRBj - BMREntryMaster

Found 1 Document (2.282 seconds)

BMRB: 15083

2O8K

NMR Structure of the Sigma-54 RpoN Domain Bound to the-24 Promoter Element

Authors

Doucleff, M., Pelton, J.G., Lee, P.S., Wemmer, D.E.

Assembly

SIGMA-54 RPON DOMAIN-DNA COMPLEX

Entity

1. NIRB SIGMA-54 BINDING SITE NON-TEMPLATE STRAND (polymer, Thiol state: not present), 14 monomers, 4315.733 Da Detail

TTTTGGCACG TTTC

2. NIRB SIGMA-54 BINDING SITE TEMPLATE STRAND (polymer, Thiol state: not present), 14 monomers, 4369.817 Da Detail

GAAACGTGCC AAAA

3. RNA POLYMERASE SIGMA FACTOR RPON (polymer, Thiol state: not present), 63 monomers, 7472.671 Da Detail

HMLTQGELMK LIKEIVENED KRKPYSDQEI ANILKEKGFK VARRTVAKYR EMLGIPSSRE RRI

Total weight

16158.221 Da

Max. entity weight

7472.671 Da

Source organism

Aquifex aeolicus

Exptl. method

solution NMR

Refine. method

docking, rigid-body minimization,

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 81.5 %, Completeness (bb): 78.8 % Detail

Polymer type: polydeoxyribonucleotide polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	81.5 % (864 of 1060)	84.9 % (590 of 695)	71.0 % (213 of 300)	93.8 % (61 of 65)
Backbone	78.8 % (449 of 570)	82.7 % (267 of 323)	65.6 % (122 of 186)	98.4 % (60 of 61)
Sidechain	86.4 % (475 of 550)	86.8 % (323 of 372)	86.8 % (151 of 174)	25.0 % (1 of 4)
Aromatic	74.4 % (64 of 86)	90.1 % (64 of 71)	0.0 % (0 of 15)
Methyl	100.0 % (74 of 74)	100.0 % (41 of 41)	100.0 % (33 of 33)

1. NIRB SIGMA-54 BINDING SITE NON-TEMPLATE STRAND

TTTTGGCACG TTTC

2. NIRB SIGMA-54 BINDING SITE TEMPLATE STRAND

GAAACGTGCC AAAA

3. RNA POLYMERASE SIGMA FACTOR RPON

HMLTQGELMK LIKEIVENED KRKPYSDQEI ANILKEKGFK VARRTVAKYR EMLGIPSSRE RRI

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 6.9, Details 1 mM Sigma-54-DNA (U-15N U-13C) complex; 250 mM NaCl; 10 mM deuterated-HEPES, pH 6.9; 1 mM EDTA

#	Name	Isotope labeling	Concentration
1	NIRB SIGMA-54 BINDING SITE NON-TEMPLATE STRAND	natural abundance	1 (±0.2) mM
2	NIRB SIGMA-54 BINDING SITE TEMPLATE STRAND	natural abundance	1 (±0.2) mM
3	RNA POLYMERASE SIGMA FACTOR RPON	[U-100% 13C; U-100% 15N]	1 (±0.2) mM
4	HEPES	[U-99% 2H]	10 (±0.1) mM
5	EDTA	natural abundance	1 (±0.1) mM
6	NaCl	natural abundance	250 (±0.1) mM

Sample #2

Solvent system 90% H2O; 10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.9, Details 1 mM Sigma-54-DNA (U-15N U-13C) complex; 250 mM NaCl; 10 mM HEPES, pH 6.9; 1 mM EDTA

#	Name	Isotope labeling	Concentration
7	NIRB SIGMA-54 BINDING SITE NON-TEMPLATE STRAND	natural abundance	1 (±0.2) mM
8	NIRB SIGMA-54 BINDING SITE NON-TEMPLATE STRAND	natural abundance	1 (±0.2) mM
9	RNA POLYMERASE SIGMA FACTOR RPON	[U-100% 13C; U-100% 15N]	1 (±0.2) mM
10	HEPES	natural abundance	10 (±0.1) mM
11	EDTA	natural abundance	1 (±0.1) mM
12	NaCl	natural abundance	250 (±0.2) mM

Sample #3

Solvent system 90% H2O; 10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.9, Details 1 mM Sigma-54-DNA (U-15N) complex; 250 mM NaCl; 10 mM HEPES, pH 6.9; 1 mM EDTA

#	Name	Isotope labeling	Concentration
13	NIRB SIGMA-54 BINDING SITE NON-TEMPLATE STRAND	natural abundance	1 (±0.2) mM
14	NIRB SIGMA-54 BINDING SITE TEMPLATE STRAND	natural abundance	1 (±0.2) mM
15	RNA POLYMERASE SIGMA FACTOR RPON	natural abundance	1 (±0.2) mM
16	HEPES	natural abundance	10 (±0.1) mM
17	EDTA	natural abundance	1 (±0.1) mM
18	NaCl	natural abundance	250 (±0.1) mM

Protein Blocks Logo

Calculated from 20 models in PDB: 2O8K, Strand ID: A Detail

Release date

2007-10-16

Citation

Structural basis of DNA recognition by the alternative sigma-factor, sigma54
Doucleff, M., Pelton, J.G., Lee, P.S., Nixon, B.T., Wemmer, D.E.
J. Mol. Biol. (2007), 369, 1070-1078, PubMed 17481658 , DOI 10.1016/j.jmb.2007.04.019 , Abstract

Related entities 3. RNA POLYMERASE SIGMA FACTOR RPON, : 1 : 1 : 2 : 54 entities Detail

Experiments performed 12 experiments Detail

1 3D_C13-seperated[F1], C12-filtered[F2] NOESY

Instrument

Bruker DMX - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 318 K, pH 6.9, Details 1 mM Sigma-54-DNA (U-15N U-13C) complex; 250 mM NaCl; 10 mM deuterated-HEPES, pH 6.9; 1 mM EDTA

#	Name	Isotope labeling	Concentration
1	NIRB SIGMA-54 BINDING SITE NON-TEMPLATE STRAND	natural abundance	1 (±0.2) mM
2	NIRB SIGMA-54 BINDING SITE TEMPLATE STRAND	natural abundance	1 (±0.2) mM
3	RNA POLYMERASE SIGMA FACTOR RPON	[U-100% 13C; U-100% 15N]	1 (±0.2) mM
4	HEPES	[U-99% 2H]	10 (±0.1) mM
5	EDTA	natural abundance	1 (±0.1) mM
6	NaCl	natural abundance	250 (±0.1) mM

2 3D_C13-seperated_NOESY

Instrument

Bruker DMX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O; 10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.9, Details 1 mM Sigma-54-DNA (U-15N U-13C) complex; 250 mM NaCl; 10 mM HEPES, pH 6.9; 1 mM EDTA

#	Name	Isotope labeling	Concentration
7	NIRB SIGMA-54 BINDING SITE NON-TEMPLATE STRAND	natural abundance	1 (±0.2) mM
8	NIRB SIGMA-54 BINDING SITE NON-TEMPLATE STRAND	natural abundance	1 (±0.2) mM
9	RNA POLYMERASE SIGMA FACTOR RPON	[U-100% 13C; U-100% 15N]	1 (±0.2) mM
10	HEPES	natural abundance	10 (±0.1) mM
11	EDTA	natural abundance	1 (±0.1) mM
12	NaCl	natural abundance	250 (±0.2) mM

3 3D_15N-seperated_NOESY

Instrument

Bruker DMX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O; 10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.9, Details 1 mM Sigma-54-DNA (U-15N) complex; 250 mM NaCl; 10 mM HEPES, pH 6.9; 1 mM EDTA

#	Name	Isotope labeling	Concentration
13	NIRB SIGMA-54 BINDING SITE NON-TEMPLATE STRAND	natural abundance	1 (±0.2) mM
14	NIRB SIGMA-54 BINDING SITE TEMPLATE STRAND	natural abundance	1 (±0.2) mM
15	RNA POLYMERASE SIGMA FACTOR RPON	natural abundance	1 (±0.2) mM
16	HEPES	natural abundance	10 (±0.1) mM
17	EDTA	natural abundance	1 (±0.1) mM
18	NaCl	natural abundance	250 (±0.1) mM

4 2D_C12-filtered[F1,F2] NOESY

Instrument

Bruker DMX - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	NIRB SIGMA-54 BINDING SITE NON-TEMPLATE STRAND	natural abundance	1 (±0.2) mM
2	NIRB SIGMA-54 BINDING SITE TEMPLATE STRAND	natural abundance	1 (±0.2) mM
3	RNA POLYMERASE SIGMA FACTOR RPON	[U-100% 13C; U-100% 15N]	1 (±0.2) mM
4	HEPES	[U-99% 2H]	10 (±0.1) mM
5	EDTA	natural abundance	1 (±0.1) mM
6	NaCl	natural abundance	250 (±0.1) mM

5 2D_C12-filtered[F1] NOESY

Instrument

Bruker DMX - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	NIRB SIGMA-54 BINDING SITE NON-TEMPLATE STRAND	natural abundance	1 (±0.2) mM
2	NIRB SIGMA-54 BINDING SITE TEMPLATE STRAND	natural abundance	1 (±0.2) mM
3	RNA POLYMERASE SIGMA FACTOR RPON	[U-100% 13C; U-100% 15N]	1 (±0.2) mM
4	HEPES	[U-99% 2H]	10 (±0.1) mM
5	EDTA	natural abundance	1 (±0.1) mM
6	NaCl	natural abundance	250 (±0.1) mM

6 3D HNCA

Instrument

Bruker DMX - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
7	NIRB SIGMA-54 BINDING SITE NON-TEMPLATE STRAND	natural abundance	1 (±0.2) mM
8	NIRB SIGMA-54 BINDING SITE NON-TEMPLATE STRAND	natural abundance	1 (±0.2) mM
9	RNA POLYMERASE SIGMA FACTOR RPON	[U-100% 13C; U-100% 15N]	1 (±0.2) mM
10	HEPES	natural abundance	10 (±0.1) mM
11	EDTA	natural abundance	1 (±0.1) mM
12	NaCl	natural abundance	250 (±0.2) mM

7 3D CBCA(CO)NH

Instrument

Bruker DMX - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
7	NIRB SIGMA-54 BINDING SITE NON-TEMPLATE STRAND	natural abundance	1 (±0.2) mM
8	NIRB SIGMA-54 BINDING SITE NON-TEMPLATE STRAND	natural abundance	1 (±0.2) mM
9	RNA POLYMERASE SIGMA FACTOR RPON	[U-100% 13C; U-100% 15N]	1 (±0.2) mM
10	HEPES	natural abundance	10 (±0.1) mM
11	EDTA	natural abundance	1 (±0.1) mM
12	NaCl	natural abundance	250 (±0.2) mM

8 3D C(CO)NH

Instrument

Bruker DMX - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
7	NIRB SIGMA-54 BINDING SITE NON-TEMPLATE STRAND	natural abundance	1 (±0.2) mM
8	NIRB SIGMA-54 BINDING SITE NON-TEMPLATE STRAND	natural abundance	1 (±0.2) mM
9	RNA POLYMERASE SIGMA FACTOR RPON	[U-100% 13C; U-100% 15N]	1 (±0.2) mM
10	HEPES	natural abundance	10 (±0.1) mM
11	EDTA	natural abundance	1 (±0.1) mM
12	NaCl	natural abundance	250 (±0.2) mM

9 3D HBHA(CO)NH

Instrument

Bruker DMX - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
7	NIRB SIGMA-54 BINDING SITE NON-TEMPLATE STRAND	natural abundance	1 (±0.2) mM
8	NIRB SIGMA-54 BINDING SITE NON-TEMPLATE STRAND	natural abundance	1 (±0.2) mM
9	RNA POLYMERASE SIGMA FACTOR RPON	[U-100% 13C; U-100% 15N]	1 (±0.2) mM
10	HEPES	natural abundance	10 (±0.1) mM
11	EDTA	natural abundance	1 (±0.1) mM
12	NaCl	natural abundance	250 (±0.2) mM

10 3D HCCH-TOCSY

Instrument

Bruker DMX - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
7	NIRB SIGMA-54 BINDING SITE NON-TEMPLATE STRAND	natural abundance	1 (±0.2) mM
8	NIRB SIGMA-54 BINDING SITE NON-TEMPLATE STRAND	natural abundance	1 (±0.2) mM
9	RNA POLYMERASE SIGMA FACTOR RPON	[U-100% 13C; U-100% 15N]	1 (±0.2) mM
10	HEPES	natural abundance	10 (±0.1) mM
11	EDTA	natural abundance	1 (±0.1) mM
12	NaCl	natural abundance	250 (±0.2) mM

11 3D HCCH-TOCSY

Instrument

Bruker DMX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O; 10% D2O, Pressure 1 atm, Temperature 318 K, pH 6.9, Details 1 mM Sigma-54-DNA (U-15N U-13C) complex; 250 mM NaCl; 10 mM HEPES, pH 6.9; 1 mM EDTA

#	Name	Isotope labeling	Concentration
7	NIRB SIGMA-54 BINDING SITE NON-TEMPLATE STRAND	natural abundance	1 (±0.2) mM
8	NIRB SIGMA-54 BINDING SITE NON-TEMPLATE STRAND	natural abundance	1 (±0.2) mM
9	RNA POLYMERASE SIGMA FACTOR RPON	[U-100% 13C; U-100% 15N]	1 (±0.2) mM
10	HEPES	natural abundance	10 (±0.1) mM
11	EDTA	natural abundance	1 (±0.1) mM
12	NaCl	natural abundance	250 (±0.2) mM

12 3D HNHA

Instrument

Bruker DMX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O; 10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.9, Details 1 mM Sigma-54-DNA (U-15N) complex; 250 mM NaCl; 10 mM HEPES, pH 6.9; 1 mM EDTA

#	Name	Isotope labeling	Concentration
13	NIRB SIGMA-54 BINDING SITE NON-TEMPLATE STRAND	natural abundance	1 (±0.2) mM
14	NIRB SIGMA-54 BINDING SITE TEMPLATE STRAND	natural abundance	1 (±0.2) mM
15	RNA POLYMERASE SIGMA FACTOR RPON	natural abundance	1 (±0.2) mM
16	HEPES	natural abundance	10 (±0.1) mM
17	EDTA	natural abundance	1 (±0.1) mM
18	NaCl	natural abundance	250 (±0.1) mM

nullKeywords HELIX-TURN-HELIX, PROTEIN-DNA COMPLEX, RNA POLYMERASE, SIGMA-54, TRANSCRIPTION FACTOR

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Found 1 Document (2.282 seconds)

BMRB: 15083

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Related entities 3. RNA POLYMERASE SIGMA FACTOR RPON, : 1 : 1 : 2 : 54 entities Detail

Experiments performed 12 experiments Detail

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