BMRBj - BMREntryMaster

Found 1 Document (0.576 seconds)

BMRB: 15746

2JPF

Bpp3783_115-220

Authors

Shaw, G.S., Revington, M.J., Savichenko, A., Arrowsmith, C.H.

Assembly

BPP3783 115-120

Entity

1. BPP3783 115-120 (polymer, Thiol state: not present), 106 monomers, 12096.39 Da Detail

KQQLQEHAPS HANLDVKWLD GLRAGSMALQ GDVKVWMQNL EDLHTRRPDE FTARLQQSTD ALYSHLEAQW AKQHGTPPTA SDVVGMPQWQ EYTAMLRERF AGLDTI

Formula weight

12096.39 Da

Source organism

Bordetella parapertussis

Exptl. method

Refine. method

torsion angle dynamics, simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 91.5 %, Completeness: 74.3 %, Completeness (bb): 86.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	74.3 % (919 of 1237)	71.4 % (460 of 644)	76.4 % (363 of 475)	81.4 % (96 of 118)
Backbone	86.1 % (539 of 626)	85.0 % (181 of 213)	86.9 % (271 of 312)	86.1 % (87 of 101)
Sidechain	65.4 % (465 of 711)	64.0 % (276 of 431)	68.8 % (181 of 263)	47.1 % (8 of 17)
Aromatic	12.5 % (13 of 104)	21.2 % (11 of 52)	0.0 % (0 of 48)	50.0 % (2 of 4)
Methyl	86.1 % (93 of 108)	85.2 % (46 of 54)	87.0 % (47 of 54)

1. BPP3783 115-120

KQQLQEHAPS HANLDVKWLD GLRAGSMALQ GDVKVWMQNL EDLHTRRPDE FTARLQQSTD ALYSHLEAQW AKQHGTPPTA SDVVGMPQWQ EYTAMLRERF AGLDTI

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.7, Details pH 7.7 1x protease inhibitor cocktail

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.5 (±0.2) mM
2	NaCl	natural abundance		500 (±10.0) mM
3	TRIS	natural abundance		10 (±1.0) mM
4	Zn++	natural abundance		10 (±1.0) uM
5	Benzamidine	natural abundance		1 (±0.2) mM
6	NaN3	natural abundance		0.01 (±0.01) %

LACS Plot; CA

Referencing offset: -0.31 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: -0.31 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: 0.09 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: -0.66 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2009-11-10

Citation

Solution structure of a domain of a type three secretion system secretory protein BPP 3783 from Bordetella pertusis
Revington, M.J., Shaw, G.S., Savichenko, A., Arrowsmith, C.H.

Related entities 1. BPP3783 115-120, : 1 : 1 entities Detail

Experiments performed 13 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.7, Details pH 7.7 1x protease inhibitor cocktail

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.5 (±0.2) mM
2	NaCl	natural abundance		500 (±10.0) mM
3	TRIS	natural abundance		10 (±1.0) mM
4	Zn++	natural abundance		10 (±1.0) uM
5	Benzamidine	natural abundance		1 (±0.2) mM
6	NaN3	natural abundance		0.01 (±0.01) %

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.7, Details pH 7.7 1x protease inhibitor cocktail

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.5 (±0.2) mM
2	NaCl	natural abundance		500 (±10.0) mM
3	TRIS	natural abundance		10 (±1.0) mM
4	Zn++	natural abundance		10 (±1.0) uM
5	Benzamidine	natural abundance		1 (±0.2) mM
6	NaN3	natural abundance		0.01 (±0.01) %

3 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.7, Details pH 7.7 1x protease inhibitor cocktail

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.5 (±0.2) mM
2	NaCl	natural abundance		500 (±10.0) mM
3	TRIS	natural abundance		10 (±1.0) mM
4	Zn++	natural abundance		10 (±1.0) uM
5	Benzamidine	natural abundance		1 (±0.2) mM
6	NaN3	natural abundance		0.01 (±0.01) %

4 3D C(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.7, Details pH 7.7 1x protease inhibitor cocktail

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.5 (±0.2) mM
2	NaCl	natural abundance		500 (±10.0) mM
3	TRIS	natural abundance		10 (±1.0) mM
4	Zn++	natural abundance		10 (±1.0) uM
5	Benzamidine	natural abundance		1 (±0.2) mM
6	NaN3	natural abundance		0.01 (±0.01) %

5 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.7, Details pH 7.7 1x protease inhibitor cocktail

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.5 (±0.2) mM
2	NaCl	natural abundance		500 (±10.0) mM
3	TRIS	natural abundance		10 (±1.0) mM
4	Zn++	natural abundance		10 (±1.0) uM
5	Benzamidine	natural abundance		1 (±0.2) mM
6	NaN3	natural abundance		0.01 (±0.01) %

6 3D HNCA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.7, Details pH 7.7 1x protease inhibitor cocktail

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.5 (±0.2) mM
2	NaCl	natural abundance		500 (±10.0) mM
3	TRIS	natural abundance		10 (±1.0) mM
4	Zn++	natural abundance		10 (±1.0) uM
5	Benzamidine	natural abundance		1 (±0.2) mM
6	NaN3	natural abundance		0.01 (±0.01) %

7 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.7, Details pH 7.7 1x protease inhibitor cocktail

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.5 (±0.2) mM
2	NaCl	natural abundance		500 (±10.0) mM
3	TRIS	natural abundance		10 (±1.0) mM
4	Zn++	natural abundance		10 (±1.0) uM
5	Benzamidine	natural abundance		1 (±0.2) mM
6	NaN3	natural abundance		0.01 (±0.01) %

8 3D H(CCO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.7, Details pH 7.7 1x protease inhibitor cocktail

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.5 (±0.2) mM
2	NaCl	natural abundance		500 (±10.0) mM
3	TRIS	natural abundance		10 (±1.0) mM
4	Zn++	natural abundance		10 (±1.0) uM
5	Benzamidine	natural abundance		1 (±0.2) mM
6	NaN3	natural abundance		0.01 (±0.01) %

9 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.7, Details pH 7.7 1x protease inhibitor cocktail

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.5 (±0.2) mM
2	NaCl	natural abundance		500 (±10.0) mM
3	TRIS	natural abundance		10 (±1.0) mM
4	Zn++	natural abundance		10 (±1.0) uM
5	Benzamidine	natural abundance		1 (±0.2) mM
6	NaN3	natural abundance		0.01 (±0.01) %

10 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.7, Details pH 7.7 1x protease inhibitor cocktail

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.5 (±0.2) mM
2	NaCl	natural abundance		500 (±10.0) mM
3	TRIS	natural abundance		10 (±1.0) mM
4	Zn++	natural abundance		10 (±1.0) uM
5	Benzamidine	natural abundance		1 (±0.2) mM
6	NaN3	natural abundance		0.01 (±0.01) %

11 3D 1H-13C NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.7, Details pH 7.7 1x protease inhibitor cocktail

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.5 (±0.2) mM
2	NaCl	natural abundance		500 (±10.0) mM
3	TRIS	natural abundance		10 (±1.0) mM
4	Zn++	natural abundance		10 (±1.0) uM
5	Benzamidine	natural abundance		1 (±0.2) mM
6	NaN3	natural abundance		0.01 (±0.01) %

12 2D HBCBCGCDCEHE

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.7, Details pH 7.7 1x protease inhibitor cocktail

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.5 (±0.2) mM
2	NaCl	natural abundance		500 (±10.0) mM
3	TRIS	natural abundance		10 (±1.0) mM
4	Zn++	natural abundance		10 (±1.0) uM
5	Benzamidine	natural abundance		1 (±0.2) mM
6	NaN3	natural abundance		0.01 (±0.01) %

13 2D HBCBCGCDHD

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.7, Details pH 7.7 1x protease inhibitor cocktail

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.5 (±0.2) mM
2	NaCl	natural abundance		500 (±10.0) mM
3	TRIS	natural abundance		10 (±1.0) mM
4	Zn++	natural abundance		10 (±1.0) uM
5	Benzamidine	natural abundance		1 (±0.2) mM
6	NaN3	natural abundance		0.01 (±0.01) %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Dihedral angle restraints	combined_15746_2jpf.nef
Input source #2: Coordindates	2jpf.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--------8
MGSSHHHHHHSSGRENLYFQGKQQLQEHAPSHANLDVKWLDGLRAGSMALQGDVKVWMQNLEDLHTRRPDEFTARLQQSTDALYSHLEAQWAKQHGTPPT
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGSSHHHHHHSSGRENLYFQGKQQLQEHAPSHANLDVKWLDGLRAGSMALQGDVKVWMQNLEDLHTRRPDEFTARLQQSTDALYSHLEAQWAKQHGTPPT
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

0--------90-------100------
ASDVVGMPQWQEYTAMLRERFAGLDTI
|||||||||||||||||||||||||||
ASDVVGMPQWQEYTAMLRERFAGLDTI
-------110-------120-------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	127	0	0	100.0

Content subtype: combined_15746_2jpf.nef

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	921		75.6 (chain: A, length: 127)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_7	OK	118 (118)	.	52.8 (chain: A, length: 127)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 127, Sequence coverage: 75.6%
- Total number of assignments
  - ¹H chemical shifts: 468
  - ¹³C chemical shifts: 359
  - ¹⁵N chemical shifts: 94
- 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

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_7
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 127, Sequence coverage: 52.8%
- Total number of restraints: 118
- Total number of restraints per polymer type: 118
- Weight of restraints: 1.0 (118)
- Potential type of restraints: square-well-parabolic (118)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords all alpha helical rotein, type III secretion effector protein