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BMRB: 15353

2JS4

Solution NMR Structure of Bordetella bronchiseptica protein BB2007: Northeast Structural Genomics Consortium Target BoR54

Authors

Eletsky, A., Sukumaran, D., Wu, Y., Singarapu, K., Parish, D., Xu, D., Wang, D., Nwosu, C., Cunningham, K., Xiao, R., Liu, J., Baran, M.C., Swapna, G.V.T., Acton, T.B., Rost, B., Montelione, G.T., Szyperski, T.

Assembly

BoR54

Entity

1. BoR54 (polymer, Thiol state: all free), 70 monomers, 7875.935 Da Detail

MESRLLDILV CPVCKGRLEF QRAQAELVCN ADRLAFPVRD GVPIMLEAEA RSLDAEAPAQ PSLEHHHHHH

Formula weight

7875.935 Da

Source organism

Bordetella bronchiseptica

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 92.9 %, Completeness: 85.8 %, Completeness (bb): 87.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	85.8 % (682 of 795)	86.7 % (359 of 414)	83.7 % (261 of 312)	89.9 % (62 of 69)
Backbone	87.8 % (360 of 410)	89.1 % (122 of 137)	86.5 % (180 of 208)	89.2 % (58 of 65)
Sidechain	84.5 % (383 of 453)	85.6 % (237 of 277)	82.6 % (142 of 172)	100.0 % (4 of 4)
Aromatic	27.3 % (12 of 44)	36.4 % (8 of 22)	18.2 % (4 of 22)
Methyl	91.5 % (75 of 82)	90.2 % (37 of 41)	92.7 % (38 of 41)

1. BoR54

MESRLLDILV CPVCKGRLEF QRAQAELVCN ADRLAFPVRD GVPIMLEAEA RSLDAEAPAQ PSLEHHHHHH

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 100%N15 100%C13

#	Name	Isotope labeling	Type	Concentration
1	BoR54	[U-100% 13C; U-100% 15N]		1.3 mM
2	NaN3	natural abundance		0.02 %
3	DTT	natural abundance		100 mM
4	CaCl2	natural abundance		5 mM
5	NaCl	natural abundance		100 mM
6	MES	natural abundance		20 mM
7	H2O	natural abundance		95 %
8	D2O			5 %

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 100%N15 5%C13

#	Name	Isotope labeling	Type	Concentration
9	BoR54	[U-5% 13C; U-100% 15N]		0.8 mM
10	NaN3	natural abundance		0.02 %
11	DTT	natural abundance		100 mM
12	CaCl2	natural abundance		5 mM
13	NaCl	natural abundance		100 mM
14	MES	natural abundance		20 mM
15	H2O	natural abundance		95 %
16	D2O			5 %

LACS Plot; CA

Referencing offset: 0.02 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: 0.02 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: -0.02 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 0.39 ppm, Outliers: 4 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2JS4, Strand ID: A Detail

Release date

2007-08-09

Citation

NMR structure of the Bordetella bronchiseptica protein NP_888769.1 establishes a new phage-related protein family PF13554
Eletsky, A., Szyperski, T.
Protein Sci. (2011), 20, 1137-1144, PubMed 21520320 , DOI 10.1002/pro.641 , Abstract

Related entities 1. BoR54, : 1 : 1 : 84 entities Detail

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 100%N15 100%C13

#	Name	Isotope labeling	Type	Concentration
1	BoR54	[U-100% 13C; U-100% 15N]		1.3 mM
2	NaN3	natural abundance		0.02 %
3	DTT	natural abundance		100 mM
4	CaCl2	natural abundance		5 mM
5	NaCl	natural abundance		100 mM
6	MES	natural abundance		20 mM
7	H2O	natural abundance		95 %
8	D2O			5 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 100%N15 100%C13

#	Name	Isotope labeling	Type	Concentration
1	BoR54	[U-100% 13C; U-100% 15N]		1.3 mM
2	NaN3	natural abundance		0.02 %
3	DTT	natural abundance		100 mM
4	CaCl2	natural abundance		5 mM
5	NaCl	natural abundance		100 mM
6	MES	natural abundance		20 mM
7	H2O	natural abundance		95 %
8	D2O			5 %

3 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 100%N15 100%C13

#	Name	Isotope labeling	Type	Concentration
1	BoR54	[U-100% 13C; U-100% 15N]		1.3 mM
2	NaN3	natural abundance		0.02 %
3	DTT	natural abundance		100 mM
4	CaCl2	natural abundance		5 mM
5	NaCl	natural abundance		100 mM
6	MES	natural abundance		20 mM
7	H2O	natural abundance		95 %
8	D2O			5 %

4 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 100%N15 100%C13

#	Name	Isotope labeling	Type	Concentration
1	BoR54	[U-100% 13C; U-100% 15N]		1.3 mM
2	NaN3	natural abundance		0.02 %
3	DTT	natural abundance		100 mM
4	CaCl2	natural abundance		5 mM
5	NaCl	natural abundance		100 mM
6	MES	natural abundance		20 mM
7	H2O	natural abundance		95 %
8	D2O			5 %

5 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 100%N15 100%C13

#	Name	Isotope labeling	Type	Concentration
1	BoR54	[U-100% 13C; U-100% 15N]		1.3 mM
2	NaN3	natural abundance		0.02 %
3	DTT	natural abundance		100 mM
4	CaCl2	natural abundance		5 mM
5	NaCl	natural abundance		100 mM
6	MES	natural abundance		20 mM
7	H2O	natural abundance		95 %
8	D2O			5 %

6 3D HBHA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 100%N15 100%C13

#	Name	Isotope labeling	Type	Concentration
1	BoR54	[U-100% 13C; U-100% 15N]		1.3 mM
2	NaN3	natural abundance		0.02 %
3	DTT	natural abundance		100 mM
4	CaCl2	natural abundance		5 mM
5	NaCl	natural abundance		100 mM
6	MES	natural abundance		20 mM
7	H2O	natural abundance		95 %
8	D2O			5 %

7 3D (H)CCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 100%N15 100%C13

#	Name	Isotope labeling	Type	Concentration
1	BoR54	[U-100% 13C; U-100% 15N]		1.3 mM
2	NaN3	natural abundance		0.02 %
3	DTT	natural abundance		100 mM
4	CaCl2	natural abundance		5 mM
5	NaCl	natural abundance		100 mM
6	MES	natural abundance		20 mM
7	H2O	natural abundance		95 %
8	D2O			5 %

8 3D (H)CCH-COSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 100%N15 100%C13

#	Name	Isotope labeling	Type	Concentration
1	BoR54	[U-100% 13C; U-100% 15N]		1.3 mM
2	NaN3	natural abundance		0.02 %
3	DTT	natural abundance		100 mM
4	CaCl2	natural abundance		5 mM
5	NaCl	natural abundance		100 mM
6	MES	natural abundance		20 mM
7	H2O	natural abundance		95 %
8	D2O			5 %

9 3D 1H-13C,15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 100%N15 100%C13

#	Name	Isotope labeling	Type	Concentration
1	BoR54	[U-100% 13C; U-100% 15N]		1.3 mM
2	NaN3	natural abundance		0.02 %
3	DTT	natural abundance		100 mM
4	CaCl2	natural abundance		5 mM
5	NaCl	natural abundance		100 mM
6	MES	natural abundance		20 mM
7	H2O	natural abundance		95 %
8	D2O			5 %

10 3D (H)CCH-COSY

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 100%N15 100%C13

#	Name	Isotope labeling	Type	Concentration
1	BoR54	[U-100% 13C; U-100% 15N]		1.3 mM
2	NaN3	natural abundance		0.02 %
3	DTT	natural abundance		100 mM
4	CaCl2	natural abundance		5 mM
5	NaCl	natural abundance		100 mM
6	MES	natural abundance		20 mM
7	H2O	natural abundance		95 %
8	D2O			5 %

11 2D 1H-13C HSQC

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 100%N15 5%C13

#	Name	Isotope labeling	Type	Concentration
9	BoR54	[U-5% 13C; U-100% 15N]		0.8 mM
10	NaN3	natural abundance		0.02 %
11	DTT	natural abundance		100 mM
12	CaCl2	natural abundance		5 mM
13	NaCl	natural abundance		100 mM
14	MES	natural abundance		20 mM
15	H2O	natural abundance		95 %
16	D2O			5 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_15353_2js4.nef
Input source #2: Coordindates	2js4.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
MESRLLDILVCPVCKGRLEFQRAQAELVCNADRLAFPVRDGVPIMLEAEARSLDAEAPAQPSLEHHHHHH
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MESRLLDILVCPVCKGRLEFQRAQAELVCNADRLAFPVRDGVPIMLEAEARSLDAEAPAQPSLEHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	70	0	0	100.0

Content subtype: combined_15353_2js4.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	693		92.9 (chain: A, length: 70)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	774 (1)	noe	87.1 (chain: A, length: 70)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 70, Sequence coverage: 92.9%
- Total number of assignments
  - ¹H chemical shifts: 366
  - ¹³C chemical shifts: 262
  - ¹⁵N chemical shifts: 65
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 70, Sequence coverage: 87.1%
- Total number of restraints: 771
- Weight of restraints: 1.0 (771)
- Potential type of restraints: upper-bound-parabolic (771)
- Range of distance target values: 2.36, 8.65 (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

Keywords beta, NESG, Northeast Structural Genomics Consortium