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Found 1 Document (0.88 seconds)

BMRB: 34300

6F2X

Structural characterization of the Mycobacterium tuberculosis Protein Tyrosine Kinase A (PtkA)

Authors

Niesteruk, A., Jonker, H.R.A., Sreeramulu, S., Richter, C., Hutchison, M., Linhard, V., Schwalbe, H.

Assembly

Uncharacterized protein Rv2232

Entity

1. Uncharacterized protein Rv2232 (polymer, Thiol state: not present), 216 monomers, 22845.49 Da Detail

GESPQLVIFD LDGTLTDSAR GIVSSFRHAL NHIGAPVPEG DLATHIVGPP MHETLRAMGL GESAEEAIVA YRADYSARGW AMNSLFDGIG PLLADLRTAG VRLAVATSKA EPTARRILRH FGIEQHFEVI AGASTDGSRG SKVDVLAHAL AQLRPLPERL VMVGDRSHDV DGAAAHGIDT VVVGWGYGRA DFIDKTSTTV VTHAATIDEL REALGV

Formula weight

22845.49 Da

Source organism

Mycobacterium tuberculosis H37Rv

Exptl. method

solution NMR

Refine. method

simulated annealing with torsion angle dynamicscartesian angle dynamicsmolecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 93.5 %, Completeness: 78.7 %, Completeness (bb): 84.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	78.7 % (1826 of 2319)	77.2 % (910 of 1178)	79.2 % (734 of 927)	85.0 % (182 of 214)
Backbone	84.5 % (1080 of 1278)	85.7 % (382 of 446)	83.2 % (520 of 625)	86.0 % (178 of 207)
Sidechain	74.1 % (915 of 1234)	72.1 % (528 of 732)	77.4 % (383 of 495)	57.1 % (4 of 7)
Aromatic	70.9 % (105 of 148)	67.6 % (50 of 74)	73.6 % (53 of 72)	100.0 % (2 of 2)
Methyl	84.1 % (244 of 290)	85.5 % (124 of 145)	82.8 % (120 of 145)

1. entity 1

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 mbar, Temperature 298 K, pH 7.5, Details 0.2 mM [U-15N] PtkA, 50 mM HEPES, 300 mM sodium chloride, 10 mM DTT, 10 mM magnesium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	PtkA	[U-15N]	0.2 mM
2	HEPES	natural abundance	50 mM
3	sodium chloride	natural abundance	300 mM
4	DTT	natural abundance	10 mM
5	magnesium chloride	natural abundance	10 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 mbar, Temperature 298 K, pH 7.5, Details 0.2 mM [U-13C; U-15N] PtkA, 50 mM HEPES, 300 mM sodium chloride, 10 mM DTT, 10 mM magnesium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	PtkA	[U-13C; U-15N]	0.2 mM
7	HEPES	natural abundance	50 mM
8	sodium chloride	natural abundance	300 mM
9	DTT	natural abundance	10 mM
10	magnesium chloride	natural abundance	10 mM

LACS Plot; CA

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

Referencing offset: -0.44 ppm, Outliers: 3 Detail

LACS Plot; CB

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

Referencing offset: -0.44 ppm, Outliers: 3 Detail

LACS Plot; HA

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

Referencing offset: -0.02 ppm, Outliers: 2 Detail

LACS Plot; CO

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

Referencing offset: -0.15 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 6F2X, Strand ID: A Detail

Release date

2018-07-26

Citation 1

The domain architecture of the PtkA, the first tyrosine kinase from Mycobacterium tuberculosis differs from the conventional kinase architecture
Niesteruk, A., Jonker, H.R.A., Richter, C., Linhard, V., Sreeramulu, S., Schwalbe, H.
J. Biol. Chem. (2018), 293, 11823-11836, PubMed 29884774 , DOI 10.1074/jbc.RA117.000120 , Abstract

Show more 1 citaion

Citation 2

Structural characterization of the intrinsically disordered domain of Mycobacterium tuberculosis protein tyrosine kinase A
Niesteruk, A., Hutchison, M., Sreeramulu, S., Jonker, H.R.A., Richter, C., Abele, R., Bock, C., Schwalbe, H.
FEBS Lett. (2018), 592, 1233-1245, PubMed 29494752 , DOI 10.1002/1873-3468.13022 , Abstract

Hide non-primary 1 citaion

Related entities 1. Uncharacterized protein Rv2232, : 1 : 2 : 134 entities Detail

Experiments performed 20 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 950 MHz cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 mbar, Temperature 298 K, pH 7.5, Details 0.2 mM [U-15N] PtkA, 50 mM HEPES, 300 mM sodium chloride, 10 mM DTT, 10 mM magnesium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	PtkA	[U-15N]	0.2 mM
2	HEPES	natural abundance	50 mM
3	sodium chloride	natural abundance	300 mM
4	DTT	natural abundance	10 mM
5	magnesium chloride	natural abundance	10 mM

2 3D HNHA

Instrument

Bruker Avance - 600 MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
1	PtkA	[U-15N]	0.2 mM
2	HEPES	natural abundance	50 mM
3	sodium chloride	natural abundance	300 mM
4	DTT	natural abundance	10 mM
5	magnesium chloride	natural abundance	10 mM

3 3D HNCA

Instrument

Bruker Avance - 600 MHz cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 mbar, Temperature 298 K, pH 7.5, Details 0.2 mM [U-13C; U-15N] PtkA, 50 mM HEPES, 300 mM sodium chloride, 10 mM DTT, 10 mM magnesium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	PtkA	[U-13C; U-15N]	0.2 mM
7	HEPES	natural abundance	50 mM
8	sodium chloride	natural abundance	300 mM
9	DTT	natural abundance	10 mM
10	magnesium chloride	natural abundance	10 mM

4 3D HN(CO)CA

Instrument

Bruker Avance - 600 MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
6	PtkA	[U-13C; U-15N]	0.2 mM
7	HEPES	natural abundance	50 mM
8	sodium chloride	natural abundance	300 mM
9	DTT	natural abundance	10 mM
10	magnesium chloride	natural abundance	10 mM

5 null

6 null

7 null

8 3D HCC(CO)NH

Instrument

Bruker Avance - 600 MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
6	PtkA	[U-13C; U-15N]	0.2 mM
7	HEPES	natural abundance	50 mM
8	sodium chloride	natural abundance	300 mM
9	DTT	natural abundance	10 mM
10	magnesium chloride	natural abundance	10 mM

9 3D CC(CO)NH

Instrument

Bruker Avance - 600 MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
6	PtkA	[U-13C; U-15N]	0.2 mM
7	HEPES	natural abundance	50 mM
8	sodium chloride	natural abundance	300 mM
9	DTT	natural abundance	10 mM
10	magnesium chloride	natural abundance	10 mM

10 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
6	PtkA	[U-13C; U-15N]	0.2 mM
7	HEPES	natural abundance	50 mM
8	sodium chloride	natural abundance	300 mM
9	DTT	natural abundance	10 mM
10	magnesium chloride	natural abundance	10 mM

11 3D 1H-15N NOESY

Instrument

Bruker Avance - 950 MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
1	PtkA	[U-15N]	0.2 mM
2	HEPES	natural abundance	50 mM
3	sodium chloride	natural abundance	300 mM
4	DTT	natural abundance	10 mM
5	magnesium chloride	natural abundance	10 mM

12 null

13 null

14 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 950 MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
6	PtkA	[U-13C; U-15N]	0.2 mM
7	HEPES	natural abundance	50 mM
8	sodium chloride	natural abundance	300 mM
9	DTT	natural abundance	10 mM
10	magnesium chloride	natural abundance	10 mM

15 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 950 MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
6	PtkA	[U-13C; U-15N]	0.2 mM
7	HEPES	natural abundance	50 mM
8	sodium chloride	natural abundance	300 mM
9	DTT	natural abundance	10 mM
10	magnesium chloride	natural abundance	10 mM

16 2D 1H-15N HETNOE

Instrument

Bruker Avance - 700 MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
1	PtkA	[U-15N]	0.2 mM
2	HEPES	natural abundance	50 mM
3	sodium chloride	natural abundance	300 mM
4	DTT	natural abundance	10 mM
5	magnesium chloride	natural abundance	10 mM

17 2D 1H-15N T1

Instrument

Bruker Avance - 700 MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
1	PtkA	[U-15N]	0.2 mM
2	HEPES	natural abundance	50 mM
3	sodium chloride	natural abundance	300 mM
4	DTT	natural abundance	10 mM
5	magnesium chloride	natural abundance	10 mM

18 2D 1H-15N T2

Instrument

Bruker Avance - 700 MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
1	PtkA	[U-15N]	0.2 mM
2	HEPES	natural abundance	50 mM
3	sodium chloride	natural abundance	300 mM
4	DTT	natural abundance	10 mM
5	magnesium chloride	natural abundance	10 mM

19 2D 1H-15N IPAP-HSQC

Instrument

Bruker Avance - 700 MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
1	PtkA	[U-15N]	0.2 mM
2	HEPES	natural abundance	50 mM
3	sodium chloride	natural abundance	300 mM
4	DTT	natural abundance	10 mM
5	magnesium chloride	natural abundance	10 mM

20 2D 1H-15N IPAP-HSQC

Instrument

Bruker Avance - 700 MHz cryoprobe

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 mbar, Temperature 298 K, pH 7.5, Details 0.2 mM [U-15N] PtkA, 50 mM HEPES, 300 mM sodium chloride, 10 mM DTT, 10 mM magnesium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	PtkA	[U-15N]	0.2 mM
2	HEPES	natural abundance	50 mM
3	sodium chloride	natural abundance	300 mM
4	DTT	natural abundance	10 mM
5	magnesium chloride	natural abundance	10 mM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34300_3.str
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

Content subtype: bmr34300_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1935		87.0 (chain: 1, length: 216)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 216, Sequence coverage: 87.0%
- Total number of assignments
  - ¹H chemical shifts: 1077
  - ¹³C chemical shifts: 691
  - ¹⁵N chemical shifts: 167
- Completeness of assignments
  - Entity_assemble_ID: 1
- Peptide bond of PRO
- Tautomeric state of HIS
- 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: 1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1178	843	71.6
¹³C chemical shifts	927	691	74.5
¹⁵N chemical shifts	230	167	72.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	446	359	80.5
¹³C chemical shifts	432	334	77.3
¹⁵N chemical shifts	207	165	79.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	732	484	66.1
¹³C chemical shifts	495	357	72.1
¹⁵N chemical shifts	23	2	8.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	149	117	78.5
¹³C chemical shifts	149	117	78.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	74	52	70.3
¹³C chemical shifts	72	50	69.4
¹⁵N chemical shifts	2	2	100.0

Keywords TRANSFERASE, tyrosine kinase phosphorylation Mycobacterium tuberculosis

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Found 1 Document (0.88 seconds)

BMRB: 34300

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Uncharacterized protein Rv2232, : 1 : 2 : 134 entities Detail

Experiments performed 20 experiments Detail

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Chemical shift validation 3 contents Detail