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BMRB: 18184

2LNY

ShB peptide structure bound to negatively charged lipid-bilayer after Molecular Dynamics refinement

Authors

Assembly

ShB peptide

Entity

1. ShB peptide (polymer, Thiol state: not present), 20 monomers, 2228.532 Da Detail

MAAVAGLYGL GEDRQHRKKQ

Formula weight

2228.532 Da

Exptl. method

Refine. method

simulated annealing, molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 65.0 %, Completeness: 55.6 %, Completeness (bb): 62.3 % Detail

Polymer type: polypeptide(L)

	Total	¹³C	¹⁵N
All	55.6 % (60 of 108)	54.7 % (47 of 86)	59.1 % (13 of 22)
Backbone	62.3 % (48 of 77)	61.4 % (35 of 57)	65.0 % (13 of 20)
Sidechain	45.8 % (22 of 48)	47.8 % (22 of 46)	0.0 % (0 of 2)
Aromatic	0.0 % (0 of 6)	0.0 % (0 of 6)
Methyl	88.9 % (8 of 9)	88.9 % (8 of 9)

1. entity

MAAVAGLYGL GEDRQHRKKQ

Show sample condition

Sample

Solvent system H2O/Lipid, Temperature 280 (±3) K, pH 4.0

#	Name	Isotope labeling	Type	Concentration
1	DOPC	natural abundance		7 mM
2	Cardiolipin	natural abundance		3 mM
3	H2O	natural abundance		100 %
4	sodium citrate	natural abundance		100 mM
5	Calbiochem	natural abundance		4 mM
6	Entity	natural abundance		0.055 mg/uL

Protein Blocks Logo

Calculated from 1 models in PDB: 2LNY, Strand ID: A Detail

Release date

2012-08-05

Citation

Supramolecular structure of membrane-associated polypeptides by combining solid-state NMR and molecular dynamics simulations
Weingarth, M., Ader, C., Melquiond, A.S.J., Nand, D., Pongs, O., Becker, S., Bonvin, A., Baldus, M.
Biophys. J. (2012), 103, 29-37, PubMed 22828329 , DOI 10.1016/j.bpj.2012.05.016 , Abstract

Related entities 1. ShB peptide, : 1 : 2 : 2 entities Detail

Interaction partners 1. ShB peptide, : 6 interactors Detail

More details for 6 interactors identified by 3 citations

Experiments performed 7 experiments Detail

1 13C-13C PARISxy

Instrument

Bruker Avance - 500 MHz

Sample

State solid, Solvent system H2O/Lipid, Temperature 280 (±3) K, pH 4.0

#	Name	Isotope labeling	Type	Concentration
1	DOPC	natural abundance		7 mM
2	Cardiolipin	natural abundance		3 mM
3	H2O	natural abundance		100 %
4	sodium citrate	natural abundance		100 mM
5	Calbiochem	natural abundance		4 mM
6	Entity	natural abundance		0.055 mg/uL

2 13c-13C PDSD

Instrument

Bruker Avance - 700 MHz

Sample

State solid, Solvent system H2O/Lipid, Temperature 280 (±3) K, pH 4.0

#	Name	Isotope labeling	Type	Concentration
1	DOPC	natural abundance		7 mM
2	Cardiolipin	natural abundance		3 mM
3	H2O	natural abundance		100 %
4	sodium citrate	natural abundance		100 mM
5	Calbiochem	natural abundance		4 mM
6	Entity	natural abundance		0.055 mg/uL

3 SPECIFIC-NCA

Instrument

Bruker Avance - 700 MHz

Sample

State solid, Solvent system H2O/Lipid, Temperature 280 (±3) K, pH 4.0

#	Name	Isotope labeling	Type	Concentration
1	DOPC	natural abundance		7 mM
2	Cardiolipin	natural abundance		3 mM
3	H2O	natural abundance		100 %
4	sodium citrate	natural abundance		100 mM
5	Calbiochem	natural abundance		4 mM
6	Entity	natural abundance		0.055 mg/uL

4 SPECIFIC-NCO

Instrument

Bruker Avance - 700 MHz

Sample

State solid, Solvent system H2O/Lipid, Temperature 280 (±3) K, pH 4.0

#	Name	Isotope labeling	Type	Concentration
1	DOPC	natural abundance		7 mM
2	Cardiolipin	natural abundance		3 mM
3	H2O	natural abundance		100 %
4	sodium citrate	natural abundance		100 mM
5	Calbiochem	natural abundance		4 mM
6	Entity	natural abundance		0.055 mg/uL

5 CHHC

Instrument

Bruker Avance - 700 MHz

Sample

State solid, Solvent system H2O/Lipid, Temperature 280 (±3) K, pH 4.0

#	Name	Isotope labeling	Type	Concentration
1	DOPC	natural abundance		7 mM
2	Cardiolipin	natural abundance		3 mM
3	H2O	natural abundance		100 %
4	sodium citrate	natural abundance		100 mM
5	Calbiochem	natural abundance		4 mM
6	Entity	natural abundance		0.055 mg/uL

6 NHHC

Instrument

Bruker Avance - 700 MHz

Sample

State solid, Solvent system H2O/Lipid, Temperature 280 (±3) K, pH 4.0

#	Name	Isotope labeling	Type	Concentration
1	DOPC	natural abundance		7 mM
2	Cardiolipin	natural abundance		3 mM
3	H2O	natural abundance		100 %
4	sodium citrate	natural abundance		100 mM
5	Calbiochem	natural abundance		4 mM
6	Entity	natural abundance		0.055 mg/uL

7 HHC

Instrument

Bruker Avance - 700 MHz

Sample

State solid, Solvent system H2O/Lipid, Temperature 280 (±3) K, pH 4.0

#	Name	Isotope labeling	Type	Concentration
1	DOPC	natural abundance		7 mM
2	Cardiolipin	natural abundance		3 mM
3	H2O	natural abundance		100 %
4	sodium citrate	natural abundance		100 mM
5	Calbiochem	natural abundance		4 mM
6	Entity	natural abundance		0.055 mg/uL

NMR combined restraints 7 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18184_2lny.nef
Input source #2: Coordindates	2lny.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
MAAVAGLYGLGEDRQHRKKQ
||||||||||||||||||||
MAAVAGLYGLGEDRQHRKKQ

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	20	0	0	100.0

Content subtype: combined_18184_2lny.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	54		60.0 (chain: A, length: 20)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	12 (1)	noe	60.0 (chain: A, length: 20)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	5 (1)	undefined	35.0 (chain: A, length: 20)
3	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	4 (1)	noe	20.0 (chain: A, length: 20)
4	Distance restraints	CNS/XPLOR_distance_constraints_5	OK	5 (1)	hbond	40.0 (chain: A, length: 20)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_6	OK	21 (21)	.	60.0 (chain: A, length: 20)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 20, Sequence coverage: 60.0%
- Total number of assignments
  - ¹³C chemical shifts: 43
  - ¹⁵N chemical shifts: 11
- Completeness of assignments
  - Entity_assemble_ID: A
- 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: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 20, Sequence coverage: 60.0%
- Total number of restraints: 12
- Weight of restraints: 1.0 (12)
- Potential type of restraints: square-well-parabolic (12)
- Range of distance target values: 2.2, 2.2 (Å)
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: OK
  - Experiment type: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 20, Sequence coverage: 35.0%
  - Total number of restraints: 5
  - Weight of restraints: 1.0 (5)
  - Potential type of restraints: square-well-parabolic (5)
  - Range of distance target values: 4.0, 5.5 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_4
    - Status: Warning
    - Experiment type: noe
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 20, Sequence coverage: 20.0%
    - Total number of restraints: 4
    - Weight of restraints: 1.0 (4)
    - Potential type of restraints: square-well-parabolic (4)
    - Range of distance target values: 2.0, 2.0 (Å)
    - Distance restraints per residue
      - Chain_ID: A
    - Distance restraints on contact map
    - Saveframe: CNS/XPLOR_distance_constraints_5
      - Status: OK
      - Experiment type: hbond
      - Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 20, Sequence coverage: 40.0%
      - Total number of restraints: 5
        Total hydrogen bond restraints: 5
        O...H-x: 1
        O...h-N: 1
        Long range: 3
        O...h-N: 3
      - Weight of restraints: 1.0 (5)
        Total hydrogen bond restraints: 1.0 (5)
        O...H-x: 1.0 (1)
        O...h-N: 1.0 (1)
        Long range: 1.0 (3)
        O...h-N: 1.0 (3)
      - Potential type of restraints: square-well-parabolic (5)
        Total hydrogen bond restraints: square-well-parabolic (5)
        O...H-x: square-well-parabolic (1)
        O...h-N: square-well-parabolic (1)
        Long range: square-well-parabolic (3)
        O...h-N: square-well-parabolic (3)
      - Range of distance target values: 2.5, 3.0 (Å)
      - Histogram of distance target values
      - Distance restraints per residue
        Chain_ID: A
      - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_6
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 20, Sequence coverage: 60.0%
- Total number of restraints: 21
- Total number of restraints per polymer type: 21
- Weight of restraints: 1.0 (21)
- Potential type of restraints: square-well-parabolic (21)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords ShB peptide bound to lipid bilayer