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BMRB: 16831

2KNG

Solution structure of C-domain of Lsr2

Authors

Li, Y., Xia, B.

Assembly

C-domain of Lsr2

Entity

1. C-domain of Lsr2 (polymer, Thiol state: not present), 55 monomers, 6125.549 Da Detail

SGSGRGRGAI DREQSAAIRE WARRNGHNVS TRGRIPADVI DAYHAATLEH HHHHH

Formula weight

6125.549 Da

Source organism

Mycobacterium tuberculosis

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.5 %, Completeness: 81.7 %, Completeness (bb): 88.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	81.7 % (483 of 591)	77.5 % (237 of 306)	85.5 % (194 of 227)	89.7 % (52 of 58)
Backbone	88.1 % (289 of 328)	85.2 % (98 of 115)	89.9 % (143 of 159)	88.9 % (48 of 54)
Sidechain	76.9 % (240 of 312)	72.8 % (139 of 191)	82.9 % (97 of 117)	100.0 % (4 of 4)
Aromatic	48.1 % (25 of 52)	61.5 % (16 of 26)	32.0 % (8 of 25)	100.0 % (1 of 1)
Methyl	95.8 % (46 of 48)	91.7 % (22 of 24)	100.0 % (24 of 24)

1. Lsr2C

SGSGRGRGAI DREQSAAIRE WARRNGHNVS TRGRIPADVI DAYHAATLEH HHHHH

Show sample condition

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	Lsr2C	[U-13C; U-15N]		0.8 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	PBS Na+	natural abundance		50 mM
5	NaCl	natural abundance		50 mM

LACS Plot; CA

Referencing offset: -0.31 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.31 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.05 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: -0.51 ppm, Outliers: 3 Detail

Protein Blocks Logo

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

Release date

2010-05-10

Citation

Lsr2 is a nucleoid-associated protein that targets AT-rich sequences and virulence genes in Mycobacterium tuberculosis
Gordon, B.R.G., Li, Y., Wang, L., Sintsova, A., van Bakel, H., Tian, S., Navarre, W., Xia, B., Liu, J.
Proc. Natl. Acad. Sci. U. S. A. (2010), 107, 5154-5159, PubMed 20133735 , DOI 10.1073/pnas.0913551107 , Abstract

Entries sharing articles Swiss-Prot: 1 entries Detail

Swiss-Prot: P9WIP7 released on 2014-04-16
Title LSR2_MYCTU Entity Nucleoid-associated protein Lsr2

Related entities 1. C-domain of Lsr2, : 1 : 2 entities Detail

Experiments performed 7 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
1	Lsr2C	[U-13C; U-15N]		0.8 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	PBS Na+	natural abundance		50 mM
5	NaCl	natural abundance		50 mM

2 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	Lsr2C	[U-13C; U-15N]		0.8 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	PBS Na+	natural abundance		50 mM
5	NaCl	natural abundance		50 mM

3 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	Lsr2C	[U-13C; U-15N]		0.8 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	PBS Na+	natural abundance		50 mM
5	NaCl	natural abundance		50 mM

4 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	Lsr2C	[U-13C; U-15N]		0.8 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	PBS Na+	natural abundance		50 mM
5	NaCl	natural abundance		50 mM

5 3D HCCH-COSY

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	Lsr2C	[U-13C; U-15N]		0.8 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	PBS Na+	natural abundance		50 mM
5	NaCl	natural abundance		50 mM

6 3D 1H-15N NOESY

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	Lsr2C	[U-13C; U-15N]		0.8 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	PBS Na+	natural abundance		50 mM
5	NaCl	natural abundance		50 mM

7 3D 1H-13C NOESY

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	Lsr2C	[U-13C; U-15N]		0.8 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	PBS Na+	natural abundance		50 mM
5	NaCl	natural abundance		50 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_16831_2kng.nef
Input source #2: Coordindates	2kng.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

---70--------80--------90-------100-------110-------120
SGSGRGRGAIDREQSAAIREWARRNGHNVSTRGRIPADVIDAYHAATLEHHHHHH
|||||||||||||||||||||||||||||||||||||||||||||||||||||||
SGSGRGRGAIDREQSAAIREWARRNGHNVSTRGRIPADVIDAYHAATLEHHHHHH
--------10--------20--------30--------40--------50-----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	55	0	0	100.0

Content subtype: combined_16831_2kng.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	494		94.5 (chain: A, length: 55)
1	Distance restraints	AMBER_distance_constraints_5	Warning	2859 (1)	noe	90.9 (chain: A, length: 55)
1	Dihedral angle restraints	AMBER_dihedral_2	OK	66 (66)	.	85.5 (chain: A, length: 55)
2	Dihedral angle restraints	AMBER_dihedral_4	Warning	1 (1)	.	3.6 (chain: A, length: 55)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 55, Sequence coverage: 94.5%
- Total number of assignments
  - ¹H chemical shifts: 244
  - ¹³C chemical shifts: 196
  - ¹⁵N chemical shifts: 54
- 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: AMBER_distance_constraints_5
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 55, Sequence coverage: 90.9%
- Total number of restraints: 2782
- Weight of restraints: 1.0 (2782)
- Potential type of restraints: square-well-parabolic (2782)
- Range of distance target values: 2.45, 7.2 (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: AMBER_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 55, Sequence coverage: 85.5%
- Total number of restraints: 66
- Total number of restraints per polymer type: 66
- Weight of restraints: 1.0 (66)
- Potential type of restraints: square-well-parabolic (66)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
- Saveframe: AMBER_dihedral_4
  - Status: Warning
  - Experiment type: .
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 55, Sequence coverage: 3.6%
  - Total number of restraints: 1
  - Total number of restraints per polymer type: 1
  - Weight of restraints: 1.0 (1)
  - Potential type of restraints: square-well-parabolic (1)
  - Dihedral angle restraints per residue

Keywords DNA-binding domain