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Found 1 Document (0.878 seconds)

BMRB: 16188

2KFS

NMR structure of Rv2175c

Authors

Barthe, P., Cohen-Gonsaud, M., Roumestand, C., Molle, V.

Assembly

Rv2175c

Entity

1. Rv2175c (polymer, Thiol state: not present), 146 monomers, 15742.75 Da Detail

MPGRAPGSTL ARVGSIPAGD DVLDPDEPTY DLPRVAELLG VPVSKVAQQL REGHLVAVRR AGGVVIPQVF FTNSGQVVKS LPGLLTILHD GGYRDTEIMR WLFTPDPSLT ITRDGSRDAV SNARPVDALH AHQAREVVRR AQAMAY

Formula weight

15742.75 Da

Source organism

Mycobacterium tuberculosis H37Rv

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 84.4 %, Completeness (bb): 93.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	84.4 % (1365 of 1618)	95.7 % (800 of 836)	66.2 % (423 of 639)	99.3 % (142 of 143)
Backbone	93.3 % (795 of 852)	97.3 % (285 of 293)	88.7 % (377 of 425)	99.3 % (133 of 134)
Sidechain	75.4 % (678 of 899)	94.8 % (515 of 543)	44.4 % (154 of 347)	100.0 % (9 of 9)
Aromatic	50.0 % (41 of 82)	85.4 % (35 of 41)	12.5 % (5 of 40)	100.0 % (1 of 1)
Methyl	67.9 % (129 of 190)	100.0 % (95 of 95)	35.8 % (34 of 95)

1. Rv2175c

MPGRAPGSTL ARVGSIPAGD DVLDPDEPTY DLPRVAELLG VPVSKVAQQL REGHLVAVRR AGGVVIPQVF FTNSGQVVKS LPGLLTILHD GGYRDTEIMR WLFTPDPSLT ITRDGSRDAV SNARPVDALH AHQAREVVRR AQAMAY

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 (±0.1) K, pH 4.6 (±0.1)

#	Name	Isotope labeling	Concentration
1	Rv2175c	[U-15N]	300 (±15.0) mM
2	sodium acetate	natural abundance	10 (±0.5) mM
3	sodium chloride	natural abundance	150 (±7.5) mM
4	D2O	natural abundance	5 %
5	H2O	natural abundance	95 %

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 (±0.1) K, pH 4.6 (±0.1)

#	Name	Isotope labeling	Concentration
6	Rv2175c	[U-13C; U-15N]	300 (±15.0) mM
7	sodium acetate	natural abundance	10 (±0.5) mM
8	sodium chloride	natural abundance	150 (±7.5) mM
9	D2O	natural abundance	5 %
10	H2O	natural abundance	95 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 303 (±0.1) K, pH 4.6 (±0.1)

#	Name	Isotope labeling	Concentration
11	Rv2175c	natural abundance	300 (±15.0) mM
12	sodium acetate	natural abundance	10 (±0.5) mM
13	sodium chloride	natural abundance	150 (±7.5) mM
14	D2O	natural abundance	100 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: -0.2 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: -0.2 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: -0.15 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: -0.13 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 30 models in PDB: 2KFS, Strand ID: A Detail

Release date

2009-05-28

Citation

The Mycobacterium tuberculosis Ser/Thr kinase substrate Rv2175c is a DNA-binding protein regulated by phosphorylation
Cohen-Gonsaud, M., Barthe, P., Canova, M.J., Stagier-Simon, C., Kremer, L., Roumestand, C., Molle, V.
J. Biol. Chem. (2009), 284, 19290-19300, PubMed 19457863 , DOI 10.1074/jbc.M109.019653 , Abstract

Related entities 1. Rv2175c, : 1 : 2 entities Detail

Experiments performed 7 experiments Detail

1 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 (±0.1) K, pH 4.6 (±0.1)

#	Name	Isotope labeling	Concentration
1	Rv2175c	[U-15N]	300 (±15.0) mM
2	sodium acetate	natural abundance	10 (±0.5) mM
3	sodium chloride	natural abundance	150 (±7.5) mM
4	D2O	natural abundance	5 %
5	H2O	natural abundance	95 %

2 3D 1H-15N TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 (±0.1) K, pH 4.6 (±0.1)

#	Name	Isotope labeling	Concentration
1	Rv2175c	[U-15N]	300 (±15.0) mM
2	sodium acetate	natural abundance	10 (±0.5) mM
3	sodium chloride	natural abundance	150 (±7.5) mM
4	D2O	natural abundance	5 %
5	H2O	natural abundance	95 %

3 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 (±0.1) K, pH 4.6 (±0.1)

#	Name	Isotope labeling	Concentration
11	Rv2175c	natural abundance	300 (±15.0) mM
12	sodium acetate	natural abundance	10 (±0.5) mM
13	sodium chloride	natural abundance	150 (±7.5) mM
14	D2O	natural abundance	100 %

4 3D HNCA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 (±0.1) K, pH 4.6 (±0.1)

#	Name	Isotope labeling	Concentration
6	Rv2175c	[U-13C; U-15N]	300 (±15.0) mM
7	sodium acetate	natural abundance	10 (±0.5) mM
8	sodium chloride	natural abundance	150 (±7.5) mM
9	D2O	natural abundance	5 %
10	H2O	natural abundance	95 %

5 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 (±0.1) K, pH 4.6 (±0.1)

#	Name	Isotope labeling	Concentration
6	Rv2175c	[U-13C; U-15N]	300 (±15.0) mM
7	sodium acetate	natural abundance	10 (±0.5) mM
8	sodium chloride	natural abundance	150 (±7.5) mM
9	D2O	natural abundance	5 %
10	H2O	natural abundance	95 %

6 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 (±0.1) K, pH 4.6 (±0.1)

#	Name	Isotope labeling	Concentration
6	Rv2175c	[U-13C; U-15N]	300 (±15.0) mM
7	sodium acetate	natural abundance	10 (±0.5) mM
8	sodium chloride	natural abundance	150 (±7.5) mM
9	D2O	natural abundance	5 %
10	H2O	natural abundance	95 %

7 3D HCACO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 (±0.1) K, pH 4.6 (±0.1)

#	Name	Isotope labeling	Concentration
6	Rv2175c	[U-13C; U-15N]	300 (±15.0) mM
7	sodium acetate	natural abundance	10 (±0.5) mM
8	sodium chloride	natural abundance	150 (±7.5) mM
9	D2O	natural abundance	5 %
10	H2O	natural abundance	95 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_16188_2kfs.nef
Input source #2: Coordindates	2kfs.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

-0--------10--------20--------30--------40--------50--------60--------70--------80--------90-------1
GHMPGRAPGSTLARVGSIPAGDDVLDPDEPTYDLPRVAELLGVPVSKVAQQLREGHLVAVRRAGGVVIPQVFFTNSGQVVKSLPGLLTILHDGGYRDTEI
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GHMPGRAPGSTLARVGSIPAGDDVLDPDEPTYDLPRVAELLGVPVSKVAQQLREGHLVAVRRAGGVVIPQVFFTNSGQVVKSLPGLLTILHDGGYRDTEI
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

00-------110-------120-------130-------140------
MRWLFTPDPSLTITRDGSRDAVSNARPVDALHAHQAREVVRRAQAMAY
||||||||||||||||||||||||||||||||||||||||||||||||
MRWLFTPDPSLTITRDGSRDAVSNARPVDALHAHQAREVVRRAQAMAY
-------110-------120-------130-------140--------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	148	0	0	100.0

Content subtype: combined_16188_2kfs.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1343		98.6 (chain: A, length: 148)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	2262 (1)	noe	98.0 (chain: A, length: 148)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	207 (207)	.	85.8 (chain: A, length: 148)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 148, Sequence coverage: 98.6%
- Total number of assignments
  - ¹H chemical shifts: 822
  - ¹³C chemical shifts: 369
  - ¹⁵N chemical shifts: 152
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	845	802	94.9
¹³C chemical shifts	646	369	57.1
¹⁵N chemical shifts	159	152	95.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	298	289	97.0
¹³C chemical shifts	296	267	90.2
¹⁵N chemical shifts	136	133	97.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	547	513	93.8
¹³C chemical shifts	350	102	29.1
¹⁵N chemical shifts	23	19	82.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	98	98	100.0
¹³C chemical shifts	98	14	14.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	43	35	81.4
¹³C chemical shifts	42	0	0.0
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 148, Sequence coverage: 98.0%
- Total number of restraints: 2262
- Weight of restraints: 1.0 (2262)
- Potential type of restraints: square-well-parabolic (2262)
- Range of distance target values: 2.05, 4.04 (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_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 148, Sequence coverage: 85.8%
- Total number of restraints: 207
- Total number of restraints per polymer type: 207
- Weight of restraints: 1.0 (207)
- Potential type of restraints: square-well-parabolic (207)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords DNA binding, Phosphorylation, wHTH

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Found 1 Document (0.878 seconds)

BMRB: 16188

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Rv2175c, : 1 : 2 entities Detail

Experiments performed 7 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail