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BMRB: 18086

2LLZ

GhoS (YjdK) monomer

Authors

Lord, D., Peti, W., Page, R.

Assembly

YjdK

Entity

1. YjdK (polymer, Thiol state: all free), 100 monomers, 11662.04 Da Detail

GHMEGKNKFN TYVVSFDYPS SYSSVFLRLR SLMYDMNFSS IVADEYGIPR QLNENSFAIT TSLAASEIED LIRLKCLDLP DIDFDLNIMT VDDYFRQFYK

Formula weight

11662.04 Da

Source organism

Escherichia coli

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.0 %, Completeness: 85.0 %, Completeness (bb): 82.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	85.0 % (1019 of 1199)	97.6 % (604 of 619)	65.7 % (312 of 475)	98.1 % (103 of 105)
Backbone	82.5 % (490 of 594)	98.0 % (196 of 200)	67.0 % (199 of 297)	97.9 % (95 of 97)
Sidechain	89.2 % (626 of 702)	97.4 % (408 of 419)	76.4 % (210 of 275)	100.0 % (8 of 8)
Aromatic	49.3 % (69 of 140)	91.4 % (64 of 70)	7.1 % (5 of 70)
Methyl	100.0 % (104 of 104)	100.0 % (52 of 52)	100.0 % (52 of 52)

1. YjdK

GHMEGKNKFN TYVVSFDYPS SYSSVFLRLR SLMYDMNFSS IVADEYGIPR QLNENSFAIT TSLAASEIED LIRLKCLDLP DIDFDLNIMT VDDYFRQFYK

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	YjdK	[U-99% 13C; U-99% 15N]		1.14 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	TCEP	natural abundance		0.5 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
7	YjdK	natural abundance		1.76 mM
8	sodium phosphate	natural abundance		20 mM
9	sodium chloride	natural abundance		100 mM
10	TCEP	natural abundance		0.5 mM
11	D2O	natural abundance		100 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
12	YjdK	[U-99% 15N]		1.42 mM
13	sodium phosphate	natural abundance		20 mM
14	sodium chloride	natural abundance		100 mM
15	TCEP	natural abundance		0.5 mM
16	H2O	natural abundance		90 %
17	D2O	natural abundance		10 %

LACS Plot; CA

Referencing offset: 0.14 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: 0.14 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: -0.01 ppm, Outliers: 3 Detail

Protein Blocks Logo

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

Release date

2012-09-03

Citation

A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS
Wang, X., Lord, D.M., Cheng, H.Y., Osbourne, D.O., Hong, S.H., Sanchez-Torres, V., Quiroga, C., Zheng, K., Herrmann, T., Peti, W., Benedik, M.J., Page, R., Wood, T.K.
Nat. Chem. Biol. (2012), 8, 855-861, PubMed 22941047 , DOI 10.1038/nchembio.1062 , Abstract

Related entities 1. YjdK, : 1 : 2 : 1 entities Detail

Experiments performed 13 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
12	YjdK	[U-99% 15N]		1.42 mM
13	sodium phosphate	natural abundance		20 mM
14	sodium chloride	natural abundance		100 mM
15	TCEP	natural abundance		0.5 mM
16	H2O	natural abundance		90 %
17	D2O	natural abundance		10 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	YjdK	[U-99% 13C; U-99% 15N]		1.14 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	TCEP	natural abundance		0.5 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

3 3D HNCA

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	YjdK	[U-99% 13C; U-99% 15N]		1.14 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	TCEP	natural abundance		0.5 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

4 3D HNCACB

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	YjdK	[U-99% 13C; U-99% 15N]		1.14 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	TCEP	natural abundance		0.5 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

5 3D CBCA(CO)NH

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	YjdK	[U-99% 13C; U-99% 15N]		1.14 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	TCEP	natural abundance		0.5 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

6 3D C(CO)NH

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	YjdK	[U-99% 13C; U-99% 15N]		1.14 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	TCEP	natural abundance		0.5 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

7 3D HBHA(CO)NH

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	YjdK	[U-99% 13C; U-99% 15N]		1.14 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	TCEP	natural abundance		0.5 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

8 3D HCCH-TOCSY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	YjdK	[U-99% 13C; U-99% 15N]		1.14 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	TCEP	natural abundance		0.5 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

9 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
12	YjdK	[U-99% 15N]		1.42 mM
13	sodium phosphate	natural abundance		20 mM
14	sodium chloride	natural abundance		100 mM
15	TCEP	natural abundance		0.5 mM
16	H2O	natural abundance		90 %
17	D2O	natural abundance		10 %

10 3D 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	YjdK	[U-99% 13C; U-99% 15N]		1.14 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	TCEP	natural abundance		0.5 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

11 2D 1H-1H TOCSY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
7	YjdK	natural abundance		1.76 mM
8	sodium phosphate	natural abundance		20 mM
9	sodium chloride	natural abundance		100 mM
10	TCEP	natural abundance		0.5 mM
11	D2O	natural abundance		100 %

12 2D 1H-1H NOESY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
7	YjdK	natural abundance		1.76 mM
8	sodium phosphate	natural abundance		20 mM
9	sodium chloride	natural abundance		100 mM
10	TCEP	natural abundance		0.5 mM
11	D2O	natural abundance		100 %

13 2D 1H-1H COSY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
7	YjdK	natural abundance		1.76 mM
8	sodium phosphate	natural abundance		20 mM
9	sodium chloride	natural abundance		100 mM
10	TCEP	natural abundance		0.5 mM
11	D2O	natural abundance		100 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_18086_2llz.nef
Input source #2: Coordindates	2llz.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-------100
GHMEGKNKFNTYVVSFDYPSSYSSVFLRLRSLMYDMNFSSIVADEYGIPRQLNENSFAITTSLAASEIEDLIRLKCLDLPDIDFDLNIMTVDDYFRQFYK
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GHMEGKNKFNTYVVSFDYPSSYSSVFLRLRSLMYDMNFSSIVADEYGIPRQLNENSFAITTSLAASEIEDLIRLKCLDLPDIDFDLNIMTVDDYFRQFYK

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	100	0	0	100.0

Content subtype: combined_18086_2llz.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1007		99.0 (chain: A, length: 100)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	3342 (1)	noe	99.0 (chain: A, length: 100)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 100, Sequence coverage: 99.0%
- Total number of assignments
  - ¹H chemical shifts: 600
  - ¹³C chemical shifts: 304
  - ¹⁵N chemical shifts: 103
- 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: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 100, Sequence coverage: 99.0%
- Total number of restraints: 3332
- Weight of restraints: 1.0 (3332)
- Potential type of restraints: upper-bound-parabolic (3332)
- Range of distance target values: 2.24, 5.5 (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