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BMRB: 18533

2LUO

NMR solution structure of apo-MptpA

Authors

Stehle, T., Sreeramulu, S., Loehr, F., Richter, C., Saxena, K., Jonker, H.R.A., Schwalbe, H.

Assembly

mptpa

Entity

1. mptpa (polymer, Thiol state: all free), 164 monomers, 17948.88 Da Detail

GMSDPLHVTF VCTGNICRSP MAEKMFAQQL RHRGLGDAVR VTSAGTGNWH VGSCADERAA GVLRAHGYPT DHRAAQVGTE HLAADLLVAL DRNHARLLRQ LGVEAARVRM LRSFDPRSGT HALDVEDPYY GDHSDFEEVF AVIESALPGL HDWVDERLAR NGPS

Formula weight

17948.88 Da

Source organism

Mycobacterium tuberculosis

Exptl. method

solution NMR

Refine. method

SIMULATED ANNEALING, TORSION ANGLE DYNAMICS, MOLECULAR DYNAMICS

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 88.2 %, Completeness (bb): 84.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	88.2 % (1578 of 1789)	94.7 % (870 of 919)	78.0 % (548 of 703)	95.8 % (160 of 167)
Backbone	84.3 % (818 of 970)	97.0 % (326 of 336)	71.3 % (340 of 477)	96.8 % (152 of 157)
Sidechain	93.4 % (904 of 968)	93.3 % (544 of 583)	93.9 % (352 of 375)	80.0 % (8 of 10)
Aromatic	78.3 % (108 of 138)	78.3 % (54 of 69)	79.1 % (53 of 67)	50.0 % (1 of 2)
Methyl	100.0 % (182 of 182)	100.0 % (91 of 91)	100.0 % (91 of 91)

1. mptpa

GMSDPLHVTF VCTGNICRSP MAEKMFAQQL RHRGLGDAVR VTSAGTGNWH VGSCADERAA GVLRAHGYPT DHRAAQVGTE HLAADLLVAL DRNHARLLRQ LGVEAARVRM LRSFDPRSGT HALDVEDPYY GDHSDFEEVF AVIESALPGL HDWVDERLAR NGPS

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	mptpa	[U-100% 13C; U-100% 15N]	1.2 mM
2	arginine / glutamine	natural abundance	50 mM
3	HEPES	natural abundance	25 mM
4	DTT	natural abundance	10 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Concentration
7	mptpa	[U-100% 15N]	1.0 mM
8	arginine / glutamine	natural abundance	50 mM
9	HEPES	natural abundance	25 mM
10	DTT	natural abundance	10 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

LACS Plot; CA

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

Referencing offset: -0.46 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: -0.46 ppm, Outliers: 1 Detail

LACS Plot; HA

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

Referencing offset: 0.07 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2012-08-12

Citation

The apo-structure of the low molecular weight protein-tyrosine phosphatase A (MptpA) from Mycobacterium tuberculosis allows for better target-specific drug development
Stehle, T., Sreeramulu, S., Loehr, F., Richter, C., Saxena, K., Jonker, H.R.A., Schwalbe, H.
J. Biol. Chem. (2012), 287, 34569-34582, PubMed 22888002 , DOI 10.1074/jbc.M112.399261 , Abstract

Related entities 1. mptpa, : 1 : 4 : 114 entities Detail

Experiments performed 15 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz CryoProbe 1H,13C,15N

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Concentration
7	mptpa	[U-100% 15N]	1.0 mM
8	arginine / glutamine	natural abundance	50 mM
9	HEPES	natural abundance	25 mM
10	DTT	natural abundance	10 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 950 MHz CryoProbe 1H,13C,15N

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	mptpa	[U-100% 13C; U-100% 15N]	1.2 mM
2	arginine / glutamine	natural abundance	50 mM
3	HEPES	natural abundance	25 mM
4	DTT	natural abundance	10 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

3 3D HNCACB

Instrument

Bruker Avance - 800 MHz CryoProbe 1H,13C,15N

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	mptpa	[U-100% 13C; U-100% 15N]	1.2 mM
2	arginine / glutamine	natural abundance	50 mM
3	HEPES	natural abundance	25 mM
4	DTT	natural abundance	10 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

4 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz CryoProbe 1H,13C,15N

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	mptpa	[U-100% 13C; U-100% 15N]	1.2 mM
2	arginine / glutamine	natural abundance	50 mM
3	HEPES	natural abundance	25 mM
4	DTT	natural abundance	10 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

5 3D (H)C(NC)H

Instrument

Bruker Avance - 800 MHz CryoProbe 1H,13C,15N

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	mptpa	[U-100% 13C; U-100% 15N]	1.2 mM
2	arginine / glutamine	natural abundance	50 mM
3	HEPES	natural abundance	25 mM
4	DTT	natural abundance	10 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

6 3D HCD(CG)CB-TOCSY

Instrument

Bruker Avance - 800 MHz CryoProbe 1H,13C,15N

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	mptpa	[U-100% 13C; U-100% 15N]	1.2 mM
2	arginine / glutamine	natural abundance	50 mM
3	HEPES	natural abundance	25 mM
4	DTT	natural abundance	10 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

7 3D (H)CC(CO)NH-TOCSY

Instrument

Bruker Avance - 600 MHz CryoProbe 1H,13C,15N

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	mptpa	[U-100% 13C; U-100% 15N]	1.2 mM
2	arginine / glutamine	natural abundance	50 mM
3	HEPES	natural abundance	25 mM
4	DTT	natural abundance	10 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

8 3D (H)CB(CG)CCH-TOCSY

Instrument

Bruker Avance - 800 MHz CryoProbe 1H,13C,15N

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	mptpa	[U-100% 13C; U-100% 15N]	1.2 mM
2	arginine / glutamine	natural abundance	50 mM
3	HEPES	natural abundance	25 mM
4	DTT	natural abundance	10 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

9 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 950 MHz CryoProbe 1H,13C,15N

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	mptpa	[U-100% 13C; U-100% 15N]	1.2 mM
2	arginine / glutamine	natural abundance	50 mM
3	HEPES	natural abundance	25 mM
4	DTT	natural abundance	10 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

10 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 900 MHz CryoProbe 1H,13C,15N

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	mptpa	[U-100% 13C; U-100% 15N]	1.2 mM
2	arginine / glutamine	natural abundance	50 mM
3	HEPES	natural abundance	25 mM
4	DTT	natural abundance	10 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

11 3D 1H-15N NOESY

Instrument

Bruker Avance - 900 MHz CryoProbe 1H,13C,15N

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Concentration
7	mptpa	[U-100% 15N]	1.0 mM
8	arginine / glutamine	natural abundance	50 mM
9	HEPES	natural abundance	25 mM
10	DTT	natural abundance	10 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

12 2D (T1,T2,HetNOE) 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz CryoProbe 1H,13C,15N

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Concentration
7	mptpa	[U-100% 15N]	1.0 mM
8	arginine / glutamine	natural abundance	50 mM
9	HEPES	natural abundance	25 mM
10	DTT	natural abundance	10 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

13 2D (IPAP) 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz CryoProbe 1H,13C,15N

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Concentration
7	mptpa	[U-100% 15N]	1.0 mM
8	arginine / glutamine	natural abundance	50 mM
9	HEPES	natural abundance	25 mM
10	DTT	natural abundance	10 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

14 2D (IPAP) 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz CryoProbe 1H,13C,15N

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Concentration
7	mptpa	[U-100% 15N]	1.0 mM
8	arginine / glutamine	natural abundance	50 mM
9	HEPES	natural abundance	25 mM
10	DTT	natural abundance	10 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

15 3D HNHA

Instrument

Bruker Avance - 600 MHz CryoProbe 1H,13C,15N

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0

#	Name	Isotope labeling	Concentration
7	mptpa	[U-100% 15N]	1.0 mM
8	arginine / glutamine	natural abundance	50 mM
9	HEPES	natural abundance	25 mM
10	DTT	natural abundance	10 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

NMR combined restraints 8 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_18533_2luo.nef
Input source #2: Coordindates	2luo.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-------10
GMSDPLHVTFVCTGNICRSPMAEKMFAQQLRHRGLGDAVRVTSAGTGNWHVGSCADERAAGVLRAHGYPTDHRAAQVGTEHLAADLLVALDRNHARLLRQ
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GMSDPLHVTFVCTGNICRSPMAEKMFAQQLRHRGLGDAVRVTSAGTGNWHVGSCADERAAGVLRAHGYPTDHRAAQVGTEHLAADLLVALDRNHARLLRQ
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

0-------110-------120-------130-------140-------150-------160---
LGVEAARVRMLRSFDPRSGTHALDVEDPYYGDHSDFEEVFAVIESALPGLHDWVDERLARNGPS
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LGVEAARVRMLRSFDPRSGTHALDVEDPYYGDHSDFEEVFAVIESALPGLHDWVDERLARNGPS
-------110-------120-------130-------140-------150-------160----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	164	0	0	100.0

Content subtype: combined_18533_2luo.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1543		99.4 (chain: A, length: 164)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	6283 (1)	noe	99.4 (chain: A, length: 164)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	138 (1)	hbond	56.7 (chain: A, length: 164)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	301 (301)	.	98.2 (chain: A, length: 164)
2	Dihedral angle restraints	CNS/XPLOR_dihedral_5	OK	163 (163)	.	100.0 (chain: A, length: 164)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_7	OK	119 (119)	.	72.6 (chain: A, length: 164)
2	RDC restraints	CNS/XPLOR_dipolar_coupling_8	OK	108 (108)	.	65.9 (chain: A, length: 164)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 164, Sequence coverage: 99.4%
- Total number of assignments
  - ¹H chemical shifts: 868
  - ¹³C chemical shifts: 516
  - ¹⁵N chemical shifts: 159
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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: A

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
71	HIS	HE2	10.57

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	919	866	94.2
¹³C chemical shifts	703	516	73.4
¹⁵N chemical shifts	183	159	86.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	336	328	97.6
¹³C chemical shifts	328	163	49.7
¹⁵N chemical shifts	157	151	96.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	583	538	92.3
¹³C chemical shifts	375	353	94.1
¹⁵N chemical shifts	26	8	30.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	95	94	98.9
¹³C chemical shifts	95	94	98.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	69	54	78.3
¹³C chemical shifts	67	53	79.1
¹⁵N chemical shifts	2	1	50.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 164, Sequence coverage: 99.4%
- Total number of restraints: 6283
- Weight of restraints: 1.0 (6283)
- Potential type of restraints: square-well-parabolic (6283)
- Range of distance target values: 1.18, 2.75 (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: 164, Sequence coverage: 56.7%
  - Total number of restraints: 138
  - Weight of restraints: 1.0 (138)
  - Potential type of restraints: square-well-parabolic (138)
  - Range of distance target values: 1.9, 2.85 (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: 164, Sequence coverage: 98.2%
- Total number of restraints: 301
- Total number of restraints per polymer type: 301
- Weight of restraints: 1.0 (301)
- Potential type of restraints: square-well-parabolic (301)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
- Saveframe: CNS/XPLOR_dihedral_5
  - Status: OK
  - Experiment type: .
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 164, Sequence coverage: 100.0%
  - Total number of restraints: 163
  - Total number of restraints per polymer type: 163
  - Weight of restraints: 1.0 (163)
  - Potential type of restraints: square-well-parabolic (163)
  - Dihedral angle restraints per residue
    - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_7

Status: OK
Experiment type: .

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 164, Sequence coverage: 72.6%

0--------10--------20--------30--------40--------50--------60--------70--------80--------90-------10
GMSDPLHVTFVCTGNICRSPMAEKMFAQQLRHRGLGDAVRVTSAGTGNWHVGSCADERAAGVLRAHGYPTDHRAAQVGTEHLAADLLVALDRNHARLLRQ
 ||| |||  |         ||||| ||| ||||||||||||||||| |||||| |||| | || ||| |  |||||||||||| |||||||| ||||| 
.MSD.LHV..V.........MAEKM.AQQ.RHRGLGDAVRVTSAGTG.WHVGSC.DERA.G.LR.HGY.T..RAAQVGTEHLAA.LLVALDRN.ARLLR.
0--------10--------20--------30--------40--------50--------60--------70--------80--------90-------10

0-------110-------120-------130-------140-------150-------160---
LGVEAARVRMLRSFDPRSGTHALDVEDPYYGDHSDFEEVFAVIESALPGLHDWVDERLARNGPS
||| ||||||||||  |||  ||  || |||| |||  || | |||| ||||  ||| ||||  
LGV.AARVRMLRSF..RSG..AL..ED.YYGD.SDF..VF.V.ESAL.GLHD..DER.ARNG  
0-------110-------120-------130-------140-------150-------160-

Total number of restraints: 119
Potential type of restraints: undefined (119)
Range of observed RDC values: 100.0, -100.0 (Hz)
RDC restraints per residue
- Chain_ID: A
  None

Saveframe: CNS/XPLOR_dipolar_coupling_8

Status: OK
Experiment type: .

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 164, Sequence coverage: 65.9%

0--------10--------20--------30--------40--------50--------60--------70--------80--------90-------10
GMSDPLHVTFVCTGNICRSPMAEKMFAQQLRHRGLGDAVRVTSAGTGNWHVGSCADERAAGVLRAHGYPTDHRAAQVGTEHLAADLLVALDRNHARLLRQ
      |||||   |     ||||| ||| |||||| ||||||||||||| ||| |||| |||| ||| |  |||||||||||| |||||    ||||||
......HVTFV...N.....MAEKM.AQQ.RHRGLG.AVRVTSAGTGNWH.GSC.DERA.GVLR.HGY.T..RAAQVGTEHLAA.LLVAL....ARLLRQ
0--------10--------20--------30--------40--------50--------60--------70--------80--------90-------10

0-------110-------120-------130-------140-------150-------160---
LGVEAARVRMLRSFDPRSGTHALDVEDPYYGDHSDFEEVFAVIESALPGLHDWVDERLARNGPS
||||| ||||||||           ||  ||| ||| ||||| |||| ||||  |||       
LGVEA.RVRMLRSF...........ED..YGD.SDF.EVFAV.ESAL.GLHD..DER       
0-------110-------120-------130-------140-------150------

Total number of restraints: 108
Potential type of restraints: undefined (108)
Range of observed RDC values: 100.0, -100.0 (Hz)
RDC restraints per residue
- Chain_ID: A
  None

Keywords Low Molecular Weight Tyrosine Phosphatase, MptpA, Mycobacterium tuberculosis

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Found 1 Document (0.976 seconds)

BMRB: 18533

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. mptpa, : 1 : 4 : 114 entities Detail

Experiments performed 15 experiments Detail

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NMR combined restraints 8 contents Detail