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Found 1 Document (0.534 seconds)

BMRB: 19800

2MKY

Structure of the PrgK first periplasmic domain

Authors

Bergeron, J., McIntosh, L., Strynadka, N.

Assembly

PrgK first periplasmic domain

Entity

1. PrgK first periplasmic domain (polymer, Thiol state: not present), 58 monomers, 6525.304 Da Detail

KDKDLLKGLD QEQANEVIAV LQMHNIEANK IDSGKLGYSI TVAEPDFTAA VYWIKTYQ

Formula weight

6525.304 Da

Source organism

Salmonella enterica subsp. enterica serovar Typhimurium

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 93.1 %, Completeness (bb): 99.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	93.1 % (638 of 685)	93.2 % (330 of 354)	94.0 % (250 of 266)	89.2 % (58 of 65)
Backbone	99.1 % (343 of 346)	98.3 % (116 of 118)	100.0 % (171 of 171)	98.2 % (56 of 57)
Sidechain	88.8 % (350 of 394)	90.7 % (214 of 236)	89.3 % (134 of 150)	25.0 % (2 of 8)
Aromatic	78.0 % (39 of 50)	96.0 % (24 of 25)	58.3 % (14 of 24)	100.0 % (1 of 1)
Methyl	97.3 % (72 of 74)	97.3 % (36 of 37)	97.3 % (36 of 37)

1. entity

KDKDLLKGLD QEQANEVIAV LQMHNIEANK IDSGKLGYSI TVAEPDFTAA VYWIKTYQ

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	PrgK	[U-100% 13C; U-100% 15N]		1 mM
2	D2O	natural abundance		10 %
3	H2O	natural abundance		90 %
4	HEPES	natural abundance		25 mM

LACS Plot; CA

Referencing offset: -0.12 ppm, Outliers: 3 Detail

LACS Plot; CB

Referencing offset: -0.12 ppm, Outliers: 3 Detail

LACS Plot; HA

Referencing offset: -0.12 ppm, Outliers: 4 Detail

LACS Plot; CO

Referencing offset: -1.04 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2014-10-26

Citation

The structure of PrgK reveals structural rearrangements upon assembly of the type III secretion system basal body
Bergeron, J., Worrall, L., De, S., Sgourakis, N., Cheung, A., Lameignere, E., Okon, M., Baker, D., McIntosh, L., Strynadka, N.
Structure

Related entities 1. PrgK first periplasmic domain, : 1 : 5 : 1 : 5 entities Detail

Interaction partners 1. PrgK first periplasmic domain, : 3 interactors Detail

More details for 3 interactors identified by 1 citations

Experiments performed 12 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	PrgK	[U-100% 13C; U-100% 15N]		1 mM
2	D2O	natural abundance		10 %
3	H2O	natural abundance		90 %
4	HEPES	natural abundance		25 mM

2 3D CBCA(CO)NH

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	PrgK	[U-100% 13C; U-100% 15N]		1 mM
2	D2O	natural abundance		10 %
3	H2O	natural abundance		90 %
4	HEPES	natural abundance		25 mM

3 3D HNCO

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	PrgK	[U-100% 13C; U-100% 15N]		1 mM
2	D2O	natural abundance		10 %
3	H2O	natural abundance		90 %
4	HEPES	natural abundance		25 mM

4 3D HNCA

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	PrgK	[U-100% 13C; U-100% 15N]		1 mM
2	D2O	natural abundance		10 %
3	H2O	natural abundance		90 %
4	HEPES	natural abundance		25 mM

5 3D HNCACB

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	PrgK	[U-100% 13C; U-100% 15N]		1 mM
2	D2O	natural abundance		10 %
3	H2O	natural abundance		90 %
4	HEPES	natural abundance		25 mM

6 3D HCCH-TOCSY

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	PrgK	[U-100% 13C; U-100% 15N]		1 mM
2	D2O	natural abundance		10 %
3	H2O	natural abundance		90 %
4	HEPES	natural abundance		25 mM

7 3D HCACO

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	PrgK	[U-100% 13C; U-100% 15N]		1 mM
2	D2O	natural abundance		10 %
3	H2O	natural abundance		90 %
4	HEPES	natural abundance		25 mM

8 3D H(CCO)NH

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	PrgK	[U-100% 13C; U-100% 15N]		1 mM
2	D2O	natural abundance		10 %
3	H2O	natural abundance		90 %
4	HEPES	natural abundance		25 mM

9 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	PrgK	[U-100% 13C; U-100% 15N]		1 mM
2	D2O	natural abundance		10 %
3	H2O	natural abundance		90 %
4	HEPES	natural abundance		25 mM

10 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	PrgK	[U-100% 13C; U-100% 15N]		1 mM
2	D2O	natural abundance		10 %
3	H2O	natural abundance		90 %
4	HEPES	natural abundance		25 mM

11 3D 1H-15N NOESY

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	PrgK	[U-100% 13C; U-100% 15N]		1 mM
2	D2O	natural abundance		10 %
3	H2O	natural abundance		90 %
4	HEPES	natural abundance		25 mM

12 3D 1H-13C NOESY

Instrument

Bruker Avance - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	PrgK	[U-100% 13C; U-100% 15N]		1 mM
2	D2O	natural abundance		10 %
3	H2O	natural abundance		90 %
4	HEPES	natural abundance		25 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19800_2mky.nef
Input source #2: Coordindates	2mky.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

-20-------30--------40--------50--------60--------70------
KDKDLLKGLDQEQANEVIAVLQMHNIEANKIDSGKLGYSITVAEPDFTAAVYWIKTYQ
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
KDKDLLKGLDQEQANEVIAVLQMHNIEANKIDSGKLGYSITVAEPDFTAAVYWIKTYQ
--------10--------20--------30--------40--------50--------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	58	0	0	100.0

Content subtype: combined_19800_2mky.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	635		100.0 (chain: A, length: 58)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	107 (1)	noe	32.8 (chain: A, length: 58)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	101 (101)	.	96.6 (chain: A, length: 58)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 58, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 328
  - ¹³C chemical shifts: 250
  - ¹⁵N chemical shifts: 57
- Completeness of assignments
  - Entity_assemble_ID: A
- 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: A

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 58, Sequence coverage: 32.8%
- Total number of restraints: 107
- Weight of restraints: 1.0 (107)
- Potential type of restraints: upper-bound-parabolic (107)
- Range of distance target values: 7.0, 7.0 (Å)
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 58, Sequence coverage: 96.6%
- Total number of restraints: 101
- Total number of restraints per polymer type: 101
- Weight of restraints: 1.0 (101)
- Potential type of restraints: square-well-parabolic (101)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords macromolecular assemblies, Salmonella, Secretion systems