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BMRB: 30157

5T17

NMR structure of the E. coli protein NPr, residues 1-85

Authors

Wang, G., Li, X., Peterkofsky, A.

Assembly

Phosphocarrier protein NPr (E.C.2.7.11.-)

Entity

1. Phosphocarrier protein NPr (E.C.2.7.11.-) (polymer, Thiol state: not present), 85 monomers, 9246.503 Da Detail

MTVKQTVEIT NKLGMHARPA MKLFELMQGF DAEVLLRNDE GTEAEANSVI ALLMLDSAKG RQIEVEATGP QEEEALAAVI ALFNS

Formula weight

9246.503 Da

Source organism

Escherichia coli O157:H7

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.8 %, Completeness: 78.9 %, Completeness (bb): 94.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	78.9 % (756 of 958)	71.3 % (352 of 494)	84.7 % (316 of 373)	96.7 % (88 of 91)
Backbone	94.1 % (476 of 506)	91.3 % (158 of 173)	95.2 % (238 of 250)	96.4 % (80 of 83)
Sidechain	67.3 % (358 of 532)	60.4 % (194 of 321)	76.8 % (156 of 203)	100.0 % (8 of 8)
Aromatic	0.0 % (0 of 34)	0.0 % (0 of 17)	0.0 % (0 of 17)
Methyl	80.7 % (92 of 114)	70.2 % (40 of 57)	91.2 % (52 of 57)

1. entity 1

MTVKQTVEIT NKLGMHARPA MKLFELMQGF DAEVLLRNDE GTEAEANSVI ALLMLDSAKG RQIEVEATGP QEEEALAAVI ALFNS

Show sample condition

Sample

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 308 K, pH 7, Details 1 mM [U-13C; U-15N] NPr, 25 mM Tris, 93% H2O/7% D2O

#	Name	Isotope labeling	Type	Concentration
1	NPr	[U-13C; U-15N]		1 mM
2	Tris	natural abundance		25 mM

LACS Plot; CA

Referencing offset: -0.34 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.34 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: -0.08 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: -0.17 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 30 models in PDB: 5T17, Strand ID: A Detail

Release date

2016-09-22

Citation

Solution structure of NPr, a bacterial signal-transducing protein that controls the phosphorylation state of the potassium transporter-regulating protein IIA Ntr
Li, X., Peterkofsky, A., Wang, G.
Amino Acids (2008), 35, 531-539, PubMed 18421563 , DOI 10.1007/s00726-008-0079-9 , Abstract

Related entities 1. Phosphocarrier protein NPr (E.C.2.7.11.-), : 1 : 4 : 118 entities Detail

Experiments performed 12 experiments Detail

1 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 308 K, pH 7, Details 1 mM [U-13C; U-15N] NPr, 25 mM Tris, 93% H2O/7% D2O

#	Name	Isotope labeling	Type	Concentration
1	NPr	[U-13C; U-15N]		1 mM
2	Tris	natural abundance		25 mM

2 3D 1H-13C NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 308 K, pH 7, Details 1 mM [U-13C; U-15N] NPr, 25 mM Tris, 93% H2O/7% D2O

#	Name	Isotope labeling	Type	Concentration
1	NPr	[U-13C; U-15N]		1 mM
2	Tris	natural abundance		25 mM

3 4D HNHC NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 308 K, pH 7, Details 1 mM [U-13C; U-15N] NPr, 25 mM Tris, 93% H2O/7% D2O

#	Name	Isotope labeling	Type	Concentration
1	NPr	[U-13C; U-15N]		1 mM
2	Tris	natural abundance		25 mM

4 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 308 K, pH 7, Details 1 mM [U-13C; U-15N] NPr, 25 mM Tris, 93% H2O/7% D2O

#	Name	Isotope labeling	Type	Concentration
1	NPr	[U-13C; U-15N]		1 mM
2	Tris	natural abundance		25 mM

5 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 308 K, pH 7, Details 1 mM [U-13C; U-15N] NPr, 25 mM Tris, 93% H2O/7% D2O

#	Name	Isotope labeling	Type	Concentration
1	NPr	[U-13C; U-15N]		1 mM
2	Tris	natural abundance		25 mM

6 3D HNCA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 308 K, pH 7, Details 1 mM [U-13C; U-15N] NPr, 25 mM Tris, 93% H2O/7% D2O

#	Name	Isotope labeling	Type	Concentration
1	NPr	[U-13C; U-15N]		1 mM
2	Tris	natural abundance		25 mM

7 3D C(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 308 K, pH 7, Details 1 mM [U-13C; U-15N] NPr, 25 mM Tris, 93% H2O/7% D2O

#	Name	Isotope labeling	Type	Concentration
1	NPr	[U-13C; U-15N]		1 mM
2	Tris	natural abundance		25 mM

8 3D H(CCO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 308 K, pH 7, Details 1 mM [U-13C; U-15N] NPr, 25 mM Tris, 93% H2O/7% D2O

#	Name	Isotope labeling	Type	Concentration
1	NPr	[U-13C; U-15N]		1 mM
2	Tris	natural abundance		25 mM

9 3D HNHA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 308 K, pH 7, Details 1 mM [U-13C; U-15N] NPr, 25 mM Tris, 93% H2O/7% D2O

#	Name	Isotope labeling	Type	Concentration
1	NPr	[U-13C; U-15N]		1 mM
2	Tris	natural abundance		25 mM

10 3D HBHA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 308 K, pH 7, Details 1 mM [U-13C; U-15N] NPr, 25 mM Tris, 93% H2O/7% D2O

#	Name	Isotope labeling	Type	Concentration
1	NPr	[U-13C; U-15N]		1 mM
2	Tris	natural abundance		25 mM

11 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 308 K, pH 7, Details 1 mM [U-13C; U-15N] NPr, 25 mM Tris, 93% H2O/7% D2O

#	Name	Isotope labeling	Type	Concentration
1	NPr	[U-13C; U-15N]		1 mM
2	Tris	natural abundance		25 mM

12 3D HCCH-COSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 308 K, pH 7, Details 1 mM [U-13C; U-15N] NPr, 25 mM Tris, 93% H2O/7% D2O

#	Name	Isotope labeling	Type	Concentration
1	NPr	[U-13C; U-15N]		1 mM
2	Tris	natural abundance		25 mM

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30157_5t17.nef
Input source #2: Coordindates	5t17.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-----
MTVKQTVEITNKLGMHARPAMKLFELMQGFDAEVLLRNDEGTEAEANSVIALLMLDSAKGRQIEVEATGPQEEEALAAVIALFNS
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MTVKQTVEITNKLGMHARPAMKLFELMQGFDAEVLLRNDEGTEAEANSVIALLMLDSAKGRQIEVEATGPQEEEALAAVIALFNS

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	85	0	0	100.0

Content subtype: combined_30157_5t17.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	745		98.8 (chain: A, length: 85)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	365 (1)	noe	84.7 (chain: A, length: 85)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	860 (1)	noe	97.6 (chain: A, length: 85)
3	Distance restraints	CNS/XPLOR_distance_constraints_5	OK	78 (1)	hbond	61.2 (chain: A, length: 85)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	112 (112)	.	82.4 (chain: A, length: 85)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 85, Sequence coverage: 98.8%
- Total number of assignments
  - ¹H chemical shifts: 345
  - ¹³C chemical shifts: 312
  - ¹⁵N chemical shifts: 88
- 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: CNS/XPLOR_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 85, Sequence coverage: 84.7%
- Total number of restraints: 365
- Weight of restraints: 1.0 (365)
- Potential type of restraints: square-well-parabolic (365)
- Range of distance target values: 2.25, 3.9 (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_4
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 85, Sequence coverage: 97.6%
  - Total number of restraints: 860
  - Weight of restraints: 1.0 (860)
  - Potential type of restraints: square-well-parabolic (860)
  - Range of distance target values: 2.35, 4.15 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_5
    - Status: OK
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 85, Sequence coverage: 61.2%
    - Total number of restraints: 78
    - Weight of restraints: 1.0 (78)
    - Potential type of restraints: square-well-parabolic (78)
    - Range of distance target values: 1.75, 3.0 (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_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 85, Sequence coverage: 82.4%
- Total number of restraints: 112
- Total number of restraints per polymer type: 112
- Weight of restraints: 1.0 (112)
- Potential type of restraints: square-well-parabolic (112)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords HPr-like, PTSNtr, TRANSFERASE, biofilm, phosphotransfer protein