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BMRB: 17615

2LCL

Solution Structure of RfaH carboxyterminal domain

Authors

Burmann, B.M., Schweimer, K., Roesch, P.

Assembly

RfaH carboxyterminal domain

Entity

1. RfaH carboxyterminal domain (polymer, Thiol state: not present), 66 monomers, 7260.256 Da Detail

GAMGPKDIVD PATPYPGDKV IITEGAFEGF QAIFTEPDGE ARSMLLLNLI NKEIKHSVKN TEFRKL

Formula weight

7260.256 Da

Source organism

Escherichia coli

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 88.2 %, Completeness (bb): 83.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	88.2 % (682 of 773)	98.5 % (398 of 404)	72.7 % (221 of 304)	96.9 % (63 of 65)
Backbone	83.2 % (321 of 386)	98.5 % (131 of 133)	68.2 % (131 of 192)	96.7 % (59 of 61)
Sidechain	94.2 % (421 of 447)	98.5 % (267 of 271)	87.2 % (150 of 172)	100.0 % (4 of 4)
Aromatic	57.7 % (30 of 52)	96.2 % (25 of 26)	19.2 % (5 of 26)
Methyl	100.0 % (74 of 74)	100.0 % (37 of 37)	100.0 % (37 of 37)

1. entity

GAMGPKDIVD PATPYPGDKV IITEGAFEGF QAIFTEPDGE ARSMLLLNLI NKEIKHSVKN TEFRKL

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.5 mM RfaH-CTD solved in NMR-buffer

#	Name	Isotope labeling	Type	Concentration
1	RfaH-CTD	[U-99% 13C; U-99% 15N]		0.5 mM
2	HEPES	natural abundance		0.025 mM
3	NaCl	natural abundance		0.05 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

LACS Plot; CA

Referencing offset: -0.04 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.04 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: -0.12 ppm, Outliers: 2 Detail

Protein Blocks Logo

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

Release date

2015-07-15

Citation

An α helix to β barrel domain switch transforms the transcription factor RfaH into a translation factor
Burmann, B.M., Schweimer, K., Roesch, P., Knauer, S.H., Mooney, R.A., Sevostyanova, A., Landick, R., Artsimovitch, I.
Cell (2012), 150, 291-303, PubMed 22817892 , DOI 10.1016/j.cell.2012.05.042 , Abstract

Related entities 1. RfaH carboxyterminal domain, : 1 : 6 : 3 entities Detail

Experiments performed 8 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.5 mM RfaH-CTD solved in NMR-buffer

#	Name	Isotope labeling	Type	Concentration
1	RfaH-CTD	[U-99% 13C; U-99% 15N]		0.5 mM
2	HEPES	natural abundance		0.025 mM
3	NaCl	natural abundance		0.05 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

2 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.5 mM RfaH-CTD solved in NMR-buffer

#	Name	Isotope labeling	Type	Concentration
1	RfaH-CTD	[U-99% 13C; U-99% 15N]		0.5 mM
2	HEPES	natural abundance		0.025 mM
3	NaCl	natural abundance		0.05 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

3 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.5 mM RfaH-CTD solved in NMR-buffer

#	Name	Isotope labeling	Type	Concentration
1	RfaH-CTD	[U-99% 13C; U-99% 15N]		0.5 mM
2	HEPES	natural abundance		0.025 mM
3	NaCl	natural abundance		0.05 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

4 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.5 mM RfaH-CTD solved in NMR-buffer

#	Name	Isotope labeling	Type	Concentration
1	RfaH-CTD	[U-99% 13C; U-99% 15N]		0.5 mM
2	HEPES	natural abundance		0.025 mM
3	NaCl	natural abundance		0.05 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

5 3D C(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.5 mM RfaH-CTD solved in NMR-buffer

#	Name	Isotope labeling	Type	Concentration
1	RfaH-CTD	[U-99% 13C; U-99% 15N]		0.5 mM
2	HEPES	natural abundance		0.025 mM
3	NaCl	natural abundance		0.05 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

6 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 800 MHz equipped with CryoProbe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.5 mM RfaH-CTD solved in NMR-buffer

#	Name	Isotope labeling	Type	Concentration
1	RfaH-CTD	[U-99% 13C; U-99% 15N]		0.5 mM
2	HEPES	natural abundance		0.025 mM
3	NaCl	natural abundance		0.05 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

7 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 800 MHz equipped with CryoProbe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.5 mM RfaH-CTD solved in NMR-buffer

#	Name	Isotope labeling	Type	Concentration
1	RfaH-CTD	[U-99% 13C; U-99% 15N]		0.5 mM
2	HEPES	natural abundance		0.025 mM
3	NaCl	natural abundance		0.05 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

8 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz equipped with CryoProbe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.5 mM RfaH-CTD solved in NMR-buffer

#	Name	Isotope labeling	Type	Concentration
1	RfaH-CTD	[U-99% 13C; U-99% 15N]		0.5 mM
2	HEPES	natural abundance		0.025 mM
3	NaCl	natural abundance		0.05 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17615_2lcl.nef
Input source #2: Coordindates	2lcl.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

---100-----110-------120-------130-------140-------150-------160--
GAMGPKDIVDPATPYPGDKVIITEGAFEGFQAIFTEPDGEARSMLLLNLINKEIKHSVKNTEFRKL
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GAMGPKDIVDPATPYPGDKVIITEGAFEGFQAIFTEPDGEARSMLLLNLINKEIKHSVKNTEFRKL
--------10--------20--------30--------40--------50--------60------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	66	0	0	100.0

Content subtype: combined_17615_2lcl.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	670		100.0 (chain: A, length: 66)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1258 (1)	noe	97.0 (chain: A, length: 66)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	103 (103)	.	84.8 (chain: A, length: 66)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 66, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 397
  - ¹³C chemical shifts: 211
  - ¹⁵N chemical shifts: 62
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 66, Sequence coverage: 97.0%
- Total number of restraints: 1258
- Weight of restraints: 1.0 (1258)
- Potential type of restraints: square-well-parabolic (1258)
- Range of distance target values: 1.25, 3.0 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 66, Sequence coverage: 84.8%
- Total number of restraints: 103
- Total number of restraints per polymer type: 103
- Weight of restraints: 1.0 (103)
- Potential type of restraints: square-well-parabolic (103)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Bacterial Transcription, RfaH