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BMRB: 34286

6GSF

Solution structure of lipase binding domain LID1 of foldase from Pseudomonas aeruginosa

Authors

Viegas, A., Jaeger, K.E., Etzkorn, M., Gohlke, H., Verma, N., Dollinger, P., Kovacic, F.

Assembly

Lipase chaperone

Entity

1. Lipase chaperone (polymer), 89 monomers, 10002.11 Da Detail

MGHHHHHHLP TSFRGTSVDG SFSVDASGNL LITRDIRNLF DAFLSAVGEE PLQQSLDRLR AYIAAELQEP ARGQALALMQ QYIDYKKEL

Formula weight

10002.11 Da

Source organism

Pseudomonas aeruginosa PAO1

Exptl. method

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 93.3 %, Completeness: 83.1 %, Completeness (bb): 84.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	83.1 % (853 of 1026)	87.0 % (462 of 531)	79.3 % (318 of 401)	77.7 % (73 of 94)
Backbone	84.3 % (445 of 528)	85.1 % (154 of 181)	86.6 % (226 of 261)	75.6 % (65 of 86)
Sidechain	83.3 % (484 of 581)	88.0 % (308 of 350)	75.3 % (168 of 223)	100.0 % (8 of 8)
Aromatic	33.0 % (29 of 88)	65.9 % (29 of 44)	0.0 % (0 of 44)
Methyl	98.0 % (98 of 100)	96.0 % (48 of 50)	100.0 % (50 of 50)

1. Lipase chaperone

MGHHHHHHLP TSFRGTSVDG SFSVDASGNL LITRDIRNLF DAFLSAVGEE PLQQSLDRLR AYIAAELQEP ARGQALALMQ QYIDYKKEL

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.4, Details 530 uM [U-13C; U-15N] Lipase-interaction domain 1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Lipase-interaction domain 1	[U-13C; U-15N]		530 uM
2	Na3PO4	natural abundance		20 mM

LACS Plot; CA

Referencing offset: -0.21 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: -0.21 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: 0.01 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: -0.25 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 6GSF, Strand ID: A Detail

Release date

2018-06-17

Citation

Structural and dynamic insights revealing how lipase binding domain MD1 of Pseudomonas aeruginosa foldase affects lipase activation
Viegas, A., Dollinger, P., Verma, N., Kubiak, J., Viennet, T., Seidel, C., Gohlke, H., Etzkorn, M., Kovacic, F., Jaeger, K.E.
Sci. Rep. (2020), 10, 3578-3578, PubMed 32107397 , DOI 10.1038/s41598-020-60093-4 , Abstract

Related entities 1. Lipase chaperone, : 1 : 2 : 7 entities Detail

Experiments performed 7 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.4, Details 530 uM [U-13C; U-15N] Lipase-interaction domain 1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Lipase-interaction domain 1	[U-13C; U-15N]		530 uM
2	Na3PO4	natural abundance		20 mM

2 2D 1H-13C HSQC

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.4, Details 530 uM [U-13C; U-15N] Lipase-interaction domain 1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Lipase-interaction domain 1	[U-13C; U-15N]		530 uM
2	Na3PO4	natural abundance		20 mM

3 3D HN(CA)CO

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.4, Details 530 uM [U-13C; U-15N] Lipase-interaction domain 1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Lipase-interaction domain 1	[U-13C; U-15N]		530 uM
2	Na3PO4	natural abundance		20 mM

4 3D HNCACB

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.4, Details 530 uM [U-13C; U-15N] Lipase-interaction domain 1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Lipase-interaction domain 1	[U-13C; U-15N]		530 uM
2	Na3PO4	natural abundance		20 mM

5 3D HCCH-TOCSY

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.4, Details 530 uM [U-13C; U-15N] Lipase-interaction domain 1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Lipase-interaction domain 1	[U-13C; U-15N]		530 uM
2	Na3PO4	natural abundance		20 mM

6 3D 1H-15N NOESY

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.4, Details 530 uM [U-13C; U-15N] Lipase-interaction domain 1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Lipase-interaction domain 1	[U-13C; U-15N]		530 uM
2	Na3PO4	natural abundance		20 mM

7 3D 1H-13C NOESY

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.4, Details 530 uM [U-13C; U-15N] Lipase-interaction domain 1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Lipase-interaction domain 1	[U-13C; U-15N]		530 uM
2	Na3PO4	natural abundance		20 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_34286_6gsf.nef
Input source #2: Coordindates	6gsf.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

--60-------70--------80--------90-------100-------110-------120-------130-------140------
MGHHHHHHLPTSFRGTSVDGSFSVDASGNLLITRDIRNLFDAFLSAVGEEPLQQSLDRLRAYIAAELQEPARGQALALMQQYIDYKKEL
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGHHHHHHLPTSFRGTSVDGSFSVDASGNLLITRDIRNLFDAFLSAVGEEPLQQSLDRLRAYIAAELQEPARGQALALMQQYIDYKKEL
--------10--------20--------30--------40--------50--------60--------70--------80---------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	89	0	0	100.0

Content subtype: combined_34286_6gsf.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	863		92.1 (chain: A, length: 89)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	1524 (1)	noe	91.0 (chain: A, length: 89)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	756 (756)	.	93.3 (chain: A, length: 89)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 89, Sequence coverage: 92.1%
- Total number of assignments
  - ¹H chemical shifts: 466
  - ¹³C chemical shifts: 326
  - ¹⁵N chemical shifts: 71
- 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

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 89, Sequence coverage: 91.0%
- Total number of restraints: 1511
- Weight of restraints: 1.0 (1511)
- Potential type of restraints: upper-bound-parabolic (1511)
- Range of distance target values: 2.33, 5.5 (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

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 89, Sequence coverage: 93.3%
- Total number of restraints: 756
- Total number of restraints per polymer type: 756
- Weight of restraints: 1.0 (756)
- Potential type of restraints: square-well-parabolic (756)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords CHAPERONE, Chaperon, Lipase A, Lipase interaction domain 1, Pseudomonas aeruginosa