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Found 1 Document (0.675 seconds)

BMRB: 15645

2K0D

NMR STRUCTURE OF A MUTANT COLICIN E7 IMMUNITY PROTEIN IM7 WITH AN EXTENDED HELIX III

Authors

Figueiredo, A.MMP., Whittaker, S.B., Spronk, C.A., Knowling, S.MMP., Radford, S.E., Moore, G.R.

Assembly

Im7 mutant

Entity

1. Im7 mutant (polymer, Thiol state: not present), 101 monomers, 11076.13 Da Detail

MEHHHHHHEL KNSISDYTEA EFVQLLKEIE KENVAATDDV LDVLLEHFVK ITEHPDGTAL IYEAAARAAA NPGGDGGGPE GIVKEIKEWR AANGKPGFKQ G

Formula weight

11076.13 Da

Source organism

Escherichia coli

Exptl. method

solution NMR

Refine. method

torsion angle dynamics, simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 92.1 %, Completeness: 90.7 %, Completeness (bb): 91.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	90.7 % (1030 of 1136)	91.1 % (535 of 587)	89.7 % (399 of 445)	92.3 % (96 of 104)
Backbone	91.0 % (544 of 598)	92.3 % (192 of 208)	89.8 % (263 of 293)	91.8 % (89 of 97)
Sidechain	90.5 % (569 of 629)	90.5 % (343 of 379)	90.1 % (219 of 243)	100.0 % (7 of 7)
Aromatic	71.1 % (64 of 90)	71.1 % (32 of 45)	70.5 % (31 of 44)	100.0 % (1 of 1)
Methyl	100.0 % (108 of 108)	100.0 % (54 of 54)	100.0 % (54 of 54)

1. Im7 mutant

MEHHHHHHEL KNSISDYTEA EFVQLLKEIE KENVAATDDV LDVLLEHFVK ITEHPDGTAL IYEAAARAAA NPGGDGGGPE GIVKEIKEWR AANGKPGFKQ G

Show sample condition

Sample #1

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

#	Name	Isotope labeling	Type	Concentration
1	potassium phosphate	[U-99% 13C; U-99% 15N]		1 (±0.2) mM
2	Phosphate buffer			50 mM

Sample #2

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

#	Name	Isotope labeling	Type	Concentration
3	potassium phosphate	[U-99% 15N]		1 (±0.2) mM
4	Phosphate buffer			50 mM

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K

#	Name	Isotope labeling	Type	Concentration
5	potassium phosphate	[U-99% 13C; U-99% 15N]		1 (±0.2) mM
6	Phosphate buffer			50 mM

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: -0.24 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: -0.24 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: -0.02 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: -0.59 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 30 models in PDB: 2K0D, Strand ID: X Detail

Release date

2009-10-13

Citation

Amino acid insertion reveals a necessary three-helical intermediate in the folding pathway of the colicin E7 immunity protein Im7
Knowling, S.E., Figueiredo, A., Whittaker, S., Moore, G.R., Radford, S.E.
J. Mol. Biol. (2009), 392, 1074-1086, PubMed 19651139 , DOI 10.1016/j.jmb.2009.07.085 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 15666 released on 2009-11-09
Title Mutant Collision E7 protein IM7 with an extended helix III in M Urea

Related entities 1. Im7 mutant, : 1 : 50 entities Detail

Experiments performed 9 experiments Detail

1 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K

#	Name	Isotope labeling	Type	Concentration
1	potassium phosphate	[U-99% 13C; U-99% 15N]		1 (±0.2) mM
2	Phosphate buffer			50 mM

2 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K

#	Name	Isotope labeling	Type	Concentration
1	potassium phosphate	[U-99% 13C; U-99% 15N]		1 (±0.2) mM
2	Phosphate buffer			50 mM

3 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K

#	Name	Isotope labeling	Type	Concentration
1	potassium phosphate	[U-99% 13C; U-99% 15N]		1 (±0.2) mM
2	Phosphate buffer			50 mM

4 3D 1H-15N NOESY

Instrument

Varian INOVA - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K

#	Name	Isotope labeling	Type	Concentration
3	potassium phosphate	[U-99% 15N]		1 (±0.2) mM
4	Phosphate buffer			50 mM

5 3D 1H-15N TOCSY

Instrument

Varian INOVA - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K

#	Name	Isotope labeling	Type	Concentration
3	potassium phosphate	[U-99% 15N]		1 (±0.2) mM
4	Phosphate buffer			50 mM

6 3D 1H-13C NOESY

Instrument

Varian INOVA - 900 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K

#	Name	Isotope labeling	Type	Concentration
5	potassium phosphate	[U-99% 13C; U-99% 15N]		1 (±0.2) mM
6	Phosphate buffer			50 mM

7 3D HCCH-TOCSY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K

#	Name	Isotope labeling	Type	Concentration
1	potassium phosphate	[U-99% 13C; U-99% 15N]		1 (±0.2) mM
2	Phosphate buffer			50 mM

8 3D H(CCO)NH

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K

#	Name	Isotope labeling	Type	Concentration
1	potassium phosphate	[U-99% 13C; U-99% 15N]		1 (±0.2) mM
2	Phosphate buffer			50 mM

9 3D C(CO)NH

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K

#	Name	Isotope labeling	Type	Concentration
1	potassium phosphate	[U-99% 13C; U-99% 15N]		1 (±0.2) mM
2	Phosphate buffer			50 mM

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15645_2k0d.nef
Input source #2: Coordindates	2k0d.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): X vs Auth_asym_ID (model): X

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
X	X	101	0	0	100.0

Content subtype: combined_15645_2k0d.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1032		92.1 (chain: X, length: 101)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	3536 (1)	noe	92.1 (chain: X, length: 101)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	400 (1)	noe	58.4 (chain: X, length: 101)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	102 (102)	.	66.3 (chain: X, length: 101)
2	Dihedral angle restraints	CNS/XPLOR_dihedral_5	OK	86 (86)	.	60.4 (chain: X, length: 101)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: X, Chain length: 101, Sequence coverage: 92.1%
- Total number of assignments
  - ¹H chemical shifts: 534
  - ¹³C chemical shifts: 403
  - ¹⁵N chemical shifts: 95
- Completeness of assignments
  - Entity_assemble_ID: X
- 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: X

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
5	ASN	CG	176.819
17	GLN	CD	179.973
64	ASN	CG	177.577
86	ASN	CG	176.257
93	GLN	CD	180.725

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	587	533	90.8
¹³C chemical shifts	445	398	89.4
¹⁵N chemical shifts	106	95	89.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	208	192	92.3
¹³C chemical shifts	202	179	88.6
¹⁵N chemical shifts	97	89	91.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	379	341	90.0
¹³C chemical shifts	243	219	90.1
¹⁵N chemical shifts	9	6	66.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	55	54	98.2
¹³C chemical shifts	55	54	98.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	45	32	71.1
¹³C chemical shifts	44	31	70.5
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: X, Chain length: 101, Sequence coverage: 92.1%
- Total number of restraints: 3532
- Weight of restraints: 1.0 (3532)
- Potential type of restraints: square-well-parabolic (3532)
- Range of distance target values: 1.42, 2.85 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: X
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: OK
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: X, Chain length: 101, Sequence coverage: 58.4%
  - Total number of restraints: 400
  - Weight of restraints: 1.0 (400)
  - Potential type of restraints: square-well-parabolic (400)
  - Range of distance target values: 2.55, 3.7 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: X
  - 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: X, Chain length: 101, Sequence coverage: 66.3%
- Total number of restraints: 102
- Total number of restraints per polymer type: 102
- Weight of restraints: 1.0 (102)
- Potential type of restraints: square-well-parabolic (102)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: X
- Saveframe: CNS/XPLOR_dihedral_5
  - Status: OK
  - Experiment type: .
  - Sequence coverage of experimental data
    - Entity_assembly_ID: X, Chain length: 101, Sequence coverage: 60.4%
  - Total number of restraints: 86
  - Total number of restraints per polymer type: 86
  - Weight of restraints: 1.0 (86)
  - Potential type of restraints: square-well-parabolic (86)
  - Plot of Phi-Psi angle restraints
  - Dihedral angle restraints per residue
    - Chain_ID: X

Keywords Protein

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Found 1 Document (0.675 seconds)

BMRB: 15645

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles BMRB: 1 entries Detail

Related entities 1. Im7 mutant, : 1 : 50 entities Detail

Experiments performed 9 experiments Detail

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NMR combined restraints 6 contents Detail