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BMRB: 16066

2KC9

Structure of E. coli toxin RelE(R81A/R83A) mutant in the free state

Authors

Li, G., Zhang, Y., Inouye, M., Ikura, M.

Assembly

RelE

Entity

1. RelE (polymer, Thiol state: all free), 98 monomers, 11336.13 Da Detail

GSHMAYFLDF DERALKEWRK LGSTVREQLK KKLVEVLESP RIEANKLRGM PDCYKIKLRS SGYRLVYQVI DEKVVVFVIS VGKAEASEVY SEAVKRIL

Formula weight

11336.13 Da

Source organism

Escherichia coli

Exptl. method

Refine. method

torsion angle dynamics, simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.9 %, Completeness: 92.0 %, Completeness (bb): 94.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	92.0 % (1103 of 1199)	95.2 % (599 of 629)	87.2 % (410 of 470)	94.0 % (94 of 100)
Backbone	94.0 % (549 of 584)	94.5 % (188 of 199)	93.8 % (271 of 289)	93.8 % (90 of 96)
Sidechain	91.0 % (644 of 708)	95.6 % (411 of 430)	83.6 % (229 of 274)	100.0 % (4 of 4)
Aromatic	43.0 % (37 of 86)	83.7 % (36 of 43)	0.0 % (0 of 42)	100.0 % (1 of 1)
Methyl	100.0 % (122 of 122)	100.0 % (61 of 61)	100.0 % (61 of 61)

1. RelE

GSHMAYFLDF DERALKEWRK LGSTVREQLK KKLVEVLESP RIEANKLRGM PDCYKIKLRS SGYRLVYQVI DEKVVVFVIS VGKAEASEVY SEAVKRIL

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 296.5 (±0.1) K, pH 6.5 (±0.05)

#	Name	Isotope labeling	Type	Concentration
1	RelE	[U-13C; U-15N]		0.5 (±0.1) mM
2	sodium phosphate	natural abundance		25 mM
3	sodium chloride	natural abundance		500 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.5 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 296.5 (±0.1) K, pH 6.5 (±0.05)

#	Name	Isotope labeling	Type	Concentration
6	RelE	[U-13C; U-15N]		0.5 (±0.1) mM
7	sodium phosphate	natural abundance		25 mM
8	sodium chloride	natural abundance		500 mM
9	DTT	natural abundance		1 mM
10	sodium azide	natural abundance		0.5 mM

LACS Plot; CA

Referencing offset: 0.06 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: 0.06 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: 0.0 ppm, Outliers: 2 Detail

LACS Plot; CO

Referencing offset: -0.06 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2KC9, Strand ID: A Detail

Release date

2009-04-21

Citation

Inhibitory mechanism of Escherichia coli RelE-RelB toxin-antitoxin module involves a helix displacement near an mRNA interferase active site
Li, G., Zhang, Y., Inouye, M., Ikura, M.
J. Biol. Chem. (2009), 284, 14628-14636, PubMed 19297318 , DOI 10.1074/jbc.M809656200 , Abstract

Related entities 1. RelE, : 1 : 1 : 7 : 5 entities Detail

Interaction partners 1. RelE, : 13 interactors Detail

More details for 13 interactors identified by 3 citations

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 296.5 (±0.1) K, pH 6.5 (±0.05)

#	Name	Isotope labeling	Type	Concentration
1	RelE	[U-13C; U-15N]		0.5 (±0.1) mM
2	sodium phosphate	natural abundance		25 mM
3	sodium chloride	natural abundance		500 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.5 mM

2 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 296.5 (±0.1) K, pH 6.5 (±0.05)

#	Name	Isotope labeling	Type	Concentration
1	RelE	[U-13C; U-15N]		0.5 (±0.1) mM
2	sodium phosphate	natural abundance		25 mM
3	sodium chloride	natural abundance		500 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.5 mM

3 3D HNCACB

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 296.5 (±0.1) K, pH 6.5 (±0.05)

#	Name	Isotope labeling	Type	Concentration
1	RelE	[U-13C; U-15N]		0.5 (±0.1) mM
2	sodium phosphate	natural abundance		25 mM
3	sodium chloride	natural abundance		500 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.5 mM

4 3D C(CO)NH

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 296.5 (±0.1) K, pH 6.5 (±0.05)

#	Name	Isotope labeling	Type	Concentration
1	RelE	[U-13C; U-15N]		0.5 (±0.1) mM
2	sodium phosphate	natural abundance		25 mM
3	sodium chloride	natural abundance		500 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.5 mM

5 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 296.5 (±0.1) K, pH 6.5 (±0.05)

#	Name	Isotope labeling	Type	Concentration
1	RelE	[U-13C; U-15N]		0.5 (±0.1) mM
2	sodium phosphate	natural abundance		25 mM
3	sodium chloride	natural abundance		500 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.5 mM

6 3D H(CCO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 296.5 (±0.1) K, pH 6.5 (±0.05)

#	Name	Isotope labeling	Type	Concentration
1	RelE	[U-13C; U-15N]		0.5 (±0.1) mM
2	sodium phosphate	natural abundance		25 mM
3	sodium chloride	natural abundance		500 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.5 mM

7 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 296.5 (±0.1) K, pH 6.5 (±0.05)

#	Name	Isotope labeling	Type	Concentration
1	RelE	[U-13C; U-15N]		0.5 (±0.1) mM
2	sodium phosphate	natural abundance		25 mM
3	sodium chloride	natural abundance		500 mM
4	DTT	natural abundance		1 mM
5	sodium azide	natural abundance		0.5 mM

8 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 296.5 (±0.1) K, pH 6.5 (±0.05)

#	Name	Isotope labeling	Type	Concentration
6	RelE	[U-13C; U-15N]		0.5 (±0.1) mM
7	sodium phosphate	natural abundance		25 mM
8	sodium chloride	natural abundance		500 mM
9	DTT	natural abundance		1 mM
10	sodium azide	natural abundance		0.5 mM

9 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 296.5 (±0.1) K, pH 6.5 (±0.05)

#	Name	Isotope labeling	Type	Concentration
6	RelE	[U-13C; U-15N]		0.5 (±0.1) mM
7	sodium phosphate	natural abundance		25 mM
8	sodium chloride	natural abundance		500 mM
9	DTT	natural abundance		1 mM
10	sodium azide	natural abundance		0.5 mM

10 3D HCCH-COSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 296.5 (±0.1) K, pH 6.5 (±0.05)

#	Name	Isotope labeling	Type	Concentration
6	RelE	[U-13C; U-15N]		0.5 (±0.1) mM
7	sodium phosphate	natural abundance		25 mM
8	sodium chloride	natural abundance		500 mM
9	DTT	natural abundance		1 mM
10	sodium azide	natural abundance		0.5 mM

11 3D 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 296.5 (±0.1) K, pH 6.5 (±0.05)

#	Name	Isotope labeling	Type	Concentration
6	RelE	[U-13C; U-15N]		0.5 (±0.1) mM
7	sodium phosphate	natural abundance		25 mM
8	sodium chloride	natural abundance		500 mM
9	DTT	natural abundance		1 mM
10	sodium azide	natural abundance		0.5 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_16066_2kc9.nef
Input source #2: Coordindates	2kc9.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

-----------10--------20--------30--------40--------50--------60--------70--------80--------90-----
GSHMAYFLDFDERALKEWRKLGSTVREQLKKKLVEVLESPRIEANKLRGMPDCYKIKLRSSGYRLVYQVIDEKVVVFVISVGKAEASEVYSEAVKRIL
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSHMAYFLDFDERALKEWRKLGSTVREQLKKKLVEVLESPRIEANKLRGMPDCYKIKLRSSGYRLVYQVIDEKVVVFVISVGKAEASEVYSEAVKRIL
--------10--------20--------30--------40--------50--------60--------70--------80--------90--------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	98	0	0	100.0

Content subtype: combined_16066_2kc9.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1103		96.9 (chain: A, length: 98)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	3496 (1)	noe	96.9 (chain: A, length: 98)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	80 (1)	hbond	51.0 (chain: A, length: 98)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	124 (124)	.	80.6 (chain: A, length: 98)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 98, Sequence coverage: 96.9%
- Total number of assignments
  - ¹H chemical shifts: 600
  - ¹³C chemical shifts: 409
  - ¹⁵N chemical shifts: 94
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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: 98, Sequence coverage: 96.9%
- Total number of restraints: 3496
- Weight of restraints: 1.0 (3496)
- Potential type of restraints: square-well-parabolic (3496)
- Range of distance target values: 2.25, 3.9 (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
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 98, Sequence coverage: 51.0%
  - Total number of restraints: 80
  - Weight of restraints: 1.0 (80)
  - Potential type of restraints: square-well-parabolic (80)
  - Range of distance target values: 2.05, 3.0 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 98, Sequence coverage: 80.6%
- Total number of restraints: 124
- Total number of restraints per polymer type: 124
- Weight of restraints: 1.0 (124)
- Potential type of restraints: square-well-parabolic (124)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords mRNA interferase, RelE, Toxin, translation inhibitor