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BMRB: 19463

2N67

p87m-BMRB

Authors

Kaplan, A.R., Maciejewski, M.W., Olson, R., Alexandrescu, A.T.

Assembly

p87m-HlyIIc

Entity

1. p87m-HlyIIc (polymer, Thiol state: not present), 94 monomers, 10449.60 Da Detail

DNQKALEEQM NSINSVNDKL NKGKGKLSLS MNGNQLKATS SNAGYGISYE DKNWGIFVNG EKVYTFNEKS TVGNISNDIN KLNIKGMYIE IKQI

Formula weight

10449.6 Da

Source organism

Bacillus cereus

Exptl. method

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 94.8 %, Completeness (bb): 98.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	94.8 % (1052 of 1110)	96.4 % (563 of 584)	91.5 % (377 of 412)	98.2 % (112 of 114)
Backbone	98.9 % (558 of 564)	97.5 % (192 of 197)	99.6 % (272 of 273)	100.0 % (94 of 94)
Sidechain	91.8 % (579 of 631)	95.9 % (371 of 387)	84.8 % (190 of 224)	90.0 % (18 of 20)
Aromatic	51.6 % (33 of 64)	100.0 % (32 of 32)	0.0 % (0 of 31)	100.0 % (1 of 1)
Methyl	100.0 % (88 of 88)	100.0 % (44 of 44)	100.0 % (44 of 44)

1. p87m-HlyIIC

DNQKALEEQM NSINSVNDKL NKGKGKLSLS MNGNQLKATS SNAGYGISYE DKNWGIFVNG EKVYTFNEKS TVGNISNDIN KLNIKGMYIE IKQI

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	p87m-HlyIIC	[U-99% 13C; U-99% 15N]		0.4 mM
2	sodium phosphate	natural abundance		20 mM
3	EDTA	natural abundance		1 mM
4	AEBSF	natural abundance		1 mM
5	sodium azide	natural abundance		0.05 % w/v

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
6	p87m-HlyIIC	[U-99% 15N]		0.4 mM
7	sodium phosphate	natural abundance		20 mM
8	EDTA	natural abundance		1 mM
9	AEBSF	natural abundance		1 mM
10	sodium azide	natural abundance		0.05 % w/v

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
11	p87m-HlyIIC	[U-99% 15N]		0.4 mM
12	sodium phosphate	natural abundance		20 mM
13	EDTA	natural abundance		1 mM
14	AEBSF	natural abundance		1 mM
15	sodium azide	natural abundance		0.05 % w/v

LACS Plot; CA

Referencing offset: -0.24 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.24 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: -0.04 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 0.01 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 25 models in PDB: 2N67, Strand ID: B Detail

Release date

2013-08-27

Citation

NMR assignments for the cis and trans forms of the hemolysin II C-terminal domain
Kaplan, A.R., Maciejewski, M.W., Olson, R., Alexandrescu, A.T.
Biomol. NMR Assign. (2014), 8, 419-423, PubMed 24234348 , DOI 10.1007/s12104-013-9530-2 , Abstract

Experiments performed 14 experiments Detail

1 3D HNCACB

Instrument

Varian INOVA - 800 MHz with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	p87m-HlyIIC	[U-99% 13C; U-99% 15N]		0.4 mM
2	sodium phosphate	natural abundance		20 mM
3	EDTA	natural abundance		1 mM
4	AEBSF	natural abundance		1 mM
5	sodium azide	natural abundance		0.05 % w/v

2 3D HNCO

Instrument

Varian INOVA - 800 MHz with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	p87m-HlyIIC	[U-99% 13C; U-99% 15N]		0.4 mM
2	sodium phosphate	natural abundance		20 mM
3	EDTA	natural abundance		1 mM
4	AEBSF	natural abundance		1 mM
5	sodium azide	natural abundance		0.05 % w/v

3 3D HN(CA)CO

Instrument

Varian INOVA - 800 MHz with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	p87m-HlyIIC	[U-99% 13C; U-99% 15N]		0.4 mM
2	sodium phosphate	natural abundance		20 mM
3	EDTA	natural abundance		1 mM
4	AEBSF	natural abundance		1 mM
5	sodium azide	natural abundance		0.05 % w/v

4 2D 1H-15N HSQC

Instrument

Varian INOVA - 800 MHz with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	p87m-HlyIIC	[U-99% 13C; U-99% 15N]		0.4 mM
2	sodium phosphate	natural abundance		20 mM
3	EDTA	natural abundance		1 mM
4	AEBSF	natural abundance		1 mM
5	sodium azide	natural abundance		0.05 % w/v

5 2D 1H-13C HSQC

Instrument

Varian INOVA - 800 MHz with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	p87m-HlyIIC	[U-99% 13C; U-99% 15N]		0.4 mM
2	sodium phosphate	natural abundance		20 mM
3	EDTA	natural abundance		1 mM
4	AEBSF	natural abundance		1 mM
5	sodium azide	natural abundance		0.05 % w/v

6 2D 1H-1H TOCSY

Instrument

Varian INOVA - 800 MHz with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	p87m-HlyIIC	[U-99% 13C; U-99% 15N]		0.4 mM
2	sodium phosphate	natural abundance		20 mM
3	EDTA	natural abundance		1 mM
4	AEBSF	natural abundance		1 mM
5	sodium azide	natural abundance		0.05 % w/v

7 2D DQF-COSY

Instrument

Varian INOVA - 800 MHz with cryoprobe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
6	p87m-HlyIIC	[U-99% 15N]		0.4 mM
7	sodium phosphate	natural abundance		20 mM
8	EDTA	natural abundance		1 mM
9	AEBSF	natural abundance		1 mM
10	sodium azide	natural abundance		0.05 % w/v

8 2D 1H-1H NOESY

Instrument

Varian INOVA - 800 MHz with cryoprobe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
6	p87m-HlyIIC	[U-99% 15N]		0.4 mM
7	sodium phosphate	natural abundance		20 mM
8	EDTA	natural abundance		1 mM
9	AEBSF	natural abundance		1 mM
10	sodium azide	natural abundance		0.05 % w/v

9 3D CCH-TOCSY

Instrument

Varian INOVA - 800 MHz with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	p87m-HlyIIC	[U-99% 13C; U-99% 15N]		0.4 mM
2	sodium phosphate	natural abundance		20 mM
3	EDTA	natural abundance		1 mM
4	AEBSF	natural abundance		1 mM
5	sodium azide	natural abundance		0.05 % w/v

10 3D HNHA

Instrument

Varian INOVA - 800 MHz with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
11	p87m-HlyIIC	[U-99% 15N]		0.4 mM
12	sodium phosphate	natural abundance		20 mM
13	EDTA	natural abundance		1 mM
14	AEBSF	natural abundance		1 mM
15	sodium azide	natural abundance		0.05 % w/v

11 3D HNHB

Instrument

Varian INOVA - 800 MHz with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
11	p87m-HlyIIC	[U-99% 15N]		0.4 mM
12	sodium phosphate	natural abundance		20 mM
13	EDTA	natural abundance		1 mM
14	AEBSF	natural abundance		1 mM
15	sodium azide	natural abundance		0.05 % w/v

12 3D 1H-15N TOCSY

Instrument

Varian INOVA - 800 MHz with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
11	p87m-HlyIIC	[U-99% 15N]		0.4 mM
12	sodium phosphate	natural abundance		20 mM
13	EDTA	natural abundance		1 mM
14	AEBSF	natural abundance		1 mM
15	sodium azide	natural abundance		0.05 % w/v

13 3D 1H-13C NOESY aliphatic

Instrument

Varian INOVA - 800 MHz with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	p87m-HlyIIC	[U-99% 13C; U-99% 15N]		0.4 mM
2	sodium phosphate	natural abundance		20 mM
3	EDTA	natural abundance		1 mM
4	AEBSF	natural abundance		1 mM
5	sodium azide	natural abundance		0.05 % w/v

14 3D 1H-15N NOESY

Instrument

Varian INOVA - 800 MHz with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
11	p87m-HlyIIC	[U-99% 15N]		0.4 mM
12	sodium phosphate	natural abundance		20 mM
13	EDTA	natural abundance		1 mM
14	AEBSF	natural abundance		1 mM
15	sodium azide	natural abundance		0.05 % w/v

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19463_2n67.nef
Input source #2: Coordindates	2n67.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): B vs Auth_asym_ID (model): B

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
B	B	94	0	0	100.0

Content subtype: combined_19463_2n67.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list	Warning	1060		100.0 (chain: B, length: 94)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1545 (1)	noe	98.9 (chain: B, length: 94)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	55 (1)	hbond	43.6 (chain: B, length: 94)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	198 (198)	.	94.7 (chain: B, length: 94)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: B, Chain length: 94, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 571
  - ¹³C chemical shifts: 377
  - ¹⁵N chemical shifts: 112
- Completeness of assignments
  - Entity_assemble_ID: B
- 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: B

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: B, Chain length: 94, Sequence coverage: 98.9%
- Total number of restraints: 1545
- Weight of restraints: 1.0 (1545)
- Potential type of restraints: square-well-parabolic (1545)
- Range of distance target values: 1.66, 9.52 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: B
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_4
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: B, Chain length: 94, Sequence coverage: 43.6%
  - Total number of restraints: 55
  - Weight of restraints: 1.0 (55)
  - Potential type of restraints: square-well-parabolic (55)
  - Range of distance target values: 2.21, 3.22 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: B
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: B, Chain length: 94, Sequence coverage: 94.7%
- Total number of restraints: 198
- Total number of restraints per polymer type: 198
- Weight of restraints: 1.0 (198)
- Potential type of restraints: square-well-parabolic (198)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: B

Keywords bacterial virulence, conformational heterogeneity, membrane proteins, modular proteins, oligomerization, proline isomerization