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BMRB: 25474

2MZ6

NMR structure of Protegrin-3 (PG3) in the presence of DPC micelles

Authors

Usachev, K.S., Efimov, S.V., Kolosova, O.V., Klochkova, E.A., Aganov, A.V., Klochkov, V.V.

Assembly

Protegrin-3 (PG3)

Entity

1. Protegrin-3 (PG3) (polymer, Thiol state: all disulfide bound), 18 monomers, 2061.489 Da Detail

RGGGLCYCRR RFCVCVGR

Formula weight

2061.489 Da

Entity Connection

disulfide 2 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS6:SG	1:CYS15:SG
2	disulfide	sing	1:CYS8:SG	1:CYS13:SG

Exptl. method

Refine. method

distance geometry, simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 86.1 %, Completeness (bb): 77.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	86.1 % (173 of 201)	97.2 % (104 of 107)	73.7 % (56 of 76)	72.2 % (13 of 18)
Backbone	77.8 % (84 of 108)	97.5 % (39 of 40)	64.0 % (32 of 50)	72.2 % (13 of 18)
Sidechain	96.3 % (103 of 107)	97.0 % (65 of 67)	95.0 % (38 of 40)
Aromatic	88.9 % (16 of 18)	88.9 % (8 of 9)	88.9 % (8 of 9)
Methyl	91.7 % (11 of 12)	100.0 % (6 of 6)	83.3 % (5 of 6)

1. PG3 monomer

RGGGLCYCRR RFCVCVGR

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Temperature 293 K

#	Name	Isotope labeling	Type	Concentration
1	PG3_monomer	natural abundance		3 mg
2	TSP	[U-99% 2H]		0.01 %
3	DPC	[U-99% 2H]		20 mg

Protein Blocks Logo

Calculated from 1 models in PDB: 2MZ6, Strand ID: A, B Detail

Release date

2016-02-10

Citation

Antimicrobial peptide protegrin-3 adopt an antiparallel dimer in the presence of DPC micelles: a high-resolution NMR study
Usachev, K.S., Efimov, S.V., Kolosova, O.A., Klochkova, E.A., Aganov, A.V., Klochkov, V.V.
J. Biomol. NMR (2015), 62, 71-79, PubMed 25786621 , DOI 10.1007/s10858-015-9920-0 , Abstract

Related entities 1. Protegrin-3 (PG3), : 1 : 1 : 6 : 6 entities Detail

Experiments performed 6 experiments Detail

1 2D DQF-COSY

Instrument

Bruker Avance - 700 MHz All data were acquired at 700 MHz (Bruker Avance III HD) NMR spectrometer equipped with quadruple resonance (1H, 13C, 15N and 31P) CryoProbe.

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 293 K

#	Name	Isotope labeling	Type	Concentration
1	PG3_monomer	natural abundance		3 mg
2	TSP	[U-99% 2H]		0.01 %
3	DPC	[U-99% 2H]		20 mg

2 2D 1H-1H COSY

Instrument

Bruker Avance - 700 MHz All data were acquired at 700 MHz (Bruker Avance III HD) NMR spectrometer equipped with quadruple resonance (1H, 13C, 15N and 31P) CryoProbe.

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 293 K

#	Name	Isotope labeling	Type	Concentration
1	PG3_monomer	natural abundance		3 mg
2	TSP	[U-99% 2H]		0.01 %
3	DPC	[U-99% 2H]		20 mg

3 2D 1H-1H TOCSY

Instrument

Bruker Avance - 700 MHz All data were acquired at 700 MHz (Bruker Avance III HD) NMR spectrometer equipped with quadruple resonance (1H, 13C, 15N and 31P) CryoProbe.

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 293 K

#	Name	Isotope labeling	Type	Concentration
1	PG3_monomer	natural abundance		3 mg
2	TSP	[U-99% 2H]		0.01 %
3	DPC	[U-99% 2H]		20 mg

4 2D 1H-1H NOESY

Instrument

Bruker Avance - 700 MHz All data were acquired at 700 MHz (Bruker Avance III HD) NMR spectrometer equipped with quadruple resonance (1H, 13C, 15N and 31P) CryoProbe.

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 293 K

#	Name	Isotope labeling	Type	Concentration
1	PG3_monomer	natural abundance		3 mg
2	TSP	[U-99% 2H]		0.01 %
3	DPC	[U-99% 2H]		20 mg

5 2D 1H-15N HSQC

Instrument

Bruker Avance - 700 MHz All data were acquired at 700 MHz (Bruker Avance III HD) NMR spectrometer equipped with quadruple resonance (1H, 13C, 15N and 31P) CryoProbe.

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 293 K

#	Name	Isotope labeling	Type	Concentration
1	PG3_monomer	natural abundance		3 mg
2	TSP	[U-99% 2H]		0.01 %
3	DPC	[U-99% 2H]		20 mg

6 2D 1H-13C HSQC

Instrument

Bruker Avance - 700 MHz All data were acquired at 700 MHz (Bruker Avance III HD) NMR spectrometer equipped with quadruple resonance (1H, 13C, 15N and 31P) CryoProbe.

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 293 K

#	Name	Isotope labeling	Type	Concentration
1	PG3_monomer	natural abundance		3 mg
2	TSP	[U-99% 2H]		0.01 %
3	DPC	[U-99% 2H]		20 mg

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_25474_2mz6.nef
Input source #2: Coordindates	2mz6.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:6:CYS:SG	A:15:CYS:SG	reduced, CA 58.782, CB 24.366 ppm	reduced, CA 57.856, CB 25.187 ppm	2.02
A:8:CYS:SG	A:13:CYS:SG	reduced, CA 52.871, CB 24.84 ppm	reduced, CB 24.426 ppm	2.02
B:6:CYS:SG	B:15:CYS:SG	unknown	unknown	2.021
B:8:CYS:SG	B:13:CYS:SG	unknown	unknown	2.021

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--------
RGGGLCYCRRRFCVCVGR
||||||||||||||||||
RGGGLCYCRRRFCVCVGR

Entity_assembly_ID (NMR): B vs Auth_asym_ID (model): B

--------10--------
RGGGLCYCRRRFCVCVGR
||||||||||||||||||
RGGGLCYCRRRFCVCVGR

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	18	0	0	100.0
B	B	18	0	0	100.0

Content subtype: combined_25474_2mz6.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	4		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	180		100.0 (chain: A, length: 18)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	428 (1)	noe	100.0 (chain: A, length: 18), 100.0 (chain: B, length: 18)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	30 (1)	noe	22.2 (chain: A, length: 18), 22.2 (chain: B, length: 18)
3	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	26 (1)	hbond	38.9 (chain: A, length: 18), 38.9 (chain: B, length: 18)
4	Distance restraints	CNS/XPLOR_distance_constraints_5	Warning	10 (1)	hbond	16.7 (chain: A, length: 18), 16.7 (chain: B, length: 18)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 18, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 110
  - ¹³C chemical shifts: 56
  - ¹⁵N chemical shifts: 14
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 18, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 18, Sequence coverage: 100.0%
- Total number of restraints: 427
- Weight of restraints: 1.0 (427)
- Potential type of restraints: square-well-parabolic (427)
- Range of distance target values: 2.25, 5.0 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- 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: 18, Sequence coverage: 22.2%
    - Entity_assembly_ID: B, Chain length: 18, Sequence coverage: 22.2%
  - Total number of restraints: 30
  - Weight of restraints: 1.0 (30)
  - Potential type of restraints: square-well-parabolic (30)
  - Range of distance target values: 5.0, 5.0 (Å)
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_3
    - Status: Warning
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 18, Sequence coverage: 38.9%
      - Entity_assembly_ID: B, Chain length: 18, Sequence coverage: 38.9%
    - Total number of restraints: 26
    - Weight of restraints: 1.0 (26)
    - Potential type of restraints: square-well-parabolic (26)
    - Range of distance target values: 1.9, 2.85 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
      - Chain_ID: B
    - Distance restraints on contact map
    - Saveframe: CNS/XPLOR_distance_constraints_5
      - Status: Warning
      - Experiment type: hbond
      - Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 18, Sequence coverage: 16.7%
        Entity_assembly_ID: B, Chain length: 18, Sequence coverage: 16.7%
      - Total number of restraints: 10
        Inter-chain restraints: 2
        Total hydrogen bond restraints: 8
      - Weight of restraints: 1.0 (10)
        Inter-chain restraints: 1.0 (2)
        Total hydrogen bond restraints: 1.0 (8)
      - Potential type of restraints: square-well-parabolic (10)
        Inter-chain restraints: square-well-parabolic (2)
        Total hydrogen bond restraints: square-well-parabolic (8)
      - Range of distance target values: 1.9, 2.85 (Å)
      - Histogram of distance target values
      - Distance restraints per residue
        Chain_ID: A
        Chain_ID: B
      - Distance restraints on contact map

Keywords ANTIMICROBIAL PEPTIDE, DPC micelle, protegrin