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Found 1 Document (0.372 seconds)

BMRB: 34313

6HN9

Nicomacin-1 -- Novel antimicrobial peptides from the Arctic polychaeta Nicomache minor provide new molecular insight into biological role of the BRICHOS domain

Authors

Panteleev, P.V., Tsarev, A.V., Bolosov, I.A., Paramonov, A.S., Marggraf, M.B., Sychev, S.V., Shenkarev, Z.O., Ovchinnikova, T.V.

Assembly

Nicomacin

Entity

1. Nicomacin (polymer), 33 monomers, 3539.089 Da Detail

GFWSSVWDGA KNVGTAIIKN AKVCVYAVCV SHK

Formula weight

3539.089 Da

Source organism

Nicomache minor

Exptl. method

solution NMR

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 73.5 %, Completeness (bb): 60.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C
All	73.5 % (247 of 336)	97.3 % (183 of 188)	43.2 % (64 of 148)
Backbone	60.6 % (100 of 165)	97.1 % (67 of 69)	34.4 % (33 of 96)
Sidechain	85.1 % (171 of 201)	97.5 % (116 of 119)	67.1 % (55 of 82)
Aromatic	61.4 % (27 of 44)	95.7 % (22 of 23)	23.8 % (5 of 21)
Methyl	90.5 % (38 of 42)	100.0 % (21 of 21)	81.0 % (17 of 21)

1. entity 1

GFWSSVWDGA KNVGTAIIKN AKVCVYAVCV SHK

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 3.1, Details 0.25 mM Nicomacin, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Nicomacin	natural abundance		0.25 mM

Release date

2018-10-16

Citation

Novel Antimicrobial Peptides from the Arctic Polychaeta Nicomache minor Provide New Molecular Insight into Biological Role of the BRICHOS Domain
Panteleev, P.V., Tsarev, A.V., Bolosov, I.A., Paramonov, A.S., Marggraf, M.B., Sychev, S.V., Shenkarev, Z.O., Ovchinnikova, T.V.
Mar. Drugs (2018), 16, E401-E401, PubMed 30360541 , DOI 10.3390/md16110401 , Abstract

Experiments performed 3 experiments Detail

NMR combined restraints 8 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_34313_6hn9.nef
Input source #2: Coordindates	6hn9.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:24:CYS:SG	A:29:CYS:SG	unknown	unknown	1.849

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---
GFWSSVWDGAKNVGTAIIKNAKVCVYAVCVSHK
|||||||||||||||||||||||||||||||||
GFWSSVWDGAKNVGTAIIKNAKVCVYAVCVSHK

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	33	0	0	100.0

Content subtype: combined_34313_6hn9.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	1		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	247		100.0 (chain: A, length: 33)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	3 (1)	undefined	6.1 (chain: A, length: 33)
2	Distance restraints	DYANA/DIANA_distance_constraints_4	OK	249 (1)	noe	100.0 (chain: A, length: 33)
3	Distance restraints	DYANA/DIANA_distance_constraints_6	Warning	3 (1)	undefined	6.1 (chain: A, length: 33)
4	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	24 (1)	hbond	48.5 (chain: A, length: 33)
5	Distance restraints	DYANA/DIANA_distance_constraints_5	OK	24 (1)	hbond	48.5 (chain: A, length: 33)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_7	OK	551 (551)	.	100.0 (chain: A, length: 33)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 33, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 183
  - ¹³C chemical shifts: 64
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	188	183	97.3
¹³C chemical shifts	148	64	43.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	69	67	97.1
¹³C chemical shifts	66	9	13.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	119	116	97.5
¹³C chemical shifts	82	55	67.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	21	21	100.0
¹³C chemical shifts	21	17	81.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	23	22	95.7
¹³C chemical shifts	21	5	23.8

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_3
- Status: Warning
- Experiment type: undefined
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 33, Sequence coverage: 6.1%
- Total number of restraints: 3
- Weight of restraints: 1.0 (3)
- Potential type of restraints: upper-bound-parabolic (3)
- Range of distance target values: 2.0, 3.0 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: DYANA/DIANA_distance_constraints_4
  - Status: OK
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 33, Sequence coverage: 100.0%
  - Total number of restraints: 249
  - Weight of restraints: 1.0 (249)
  - Potential type of restraints: upper-bound-parabolic (249)
  - Range of distance target values: 2.6, 6.0 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map
  - Saveframe: DYANA/DIANA_distance_constraints_6
    - Status: Warning
    - Experiment type: undefined
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 33, Sequence coverage: 6.1%
    - Total number of restraints: 3
    - Weight of restraints: 1.0 (3)
    - Potential type of restraints: upper-bound-parabolic (3)
    - Range of distance target values: 2.1, 3.1 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
    - Distance restraints on contact map
    - Saveframe: DYANA/DIANA_distance_constraints_2
      - Status: Warning
      - Experiment type: hbond
      - Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 33, Sequence coverage: 48.5%
      - Total number of restraints: 24
        Total hydrogen bond restraints: 24
        O...H-x (too close!): 12
        O...h-N (too close!): 12
      - Weight of restraints: 1.0 (24)
        Total hydrogen bond restraints: 1.0 (24)
        O...H-x (too close!): 1.0 (12)
        O...h-N (too close!): 1.0 (12)
      - Potential type of restraints: upper-bound-parabolic (24)
        Total hydrogen bond restraints: upper-bound-parabolic (24)
        O...H-x (too close!): upper-bound-parabolic (12)
        O...h-N (too close!): upper-bound-parabolic (12)
      - Range of distance target values: 1.8, 2.7 (Å)
      - Histogram of distance target values
      - Distance restraints per residue
        Chain_ID: A
      - Distance restraints on contact map
      - Saveframe: DYANA/DIANA_distance_constraints_5
        Status: OK
        Experiment type: hbond
        Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 33, Sequence coverage: 48.5%
        Total number of restraints: 24
        Total hydrogen bond restraints: 24
        O...H-x: 12
        O...h-N: 12
        Weight of restraints: 1.0 (24)
        Total hydrogen bond restraints: 1.0 (24)
        O...H-x: 1.0 (12)
        O...h-N: 1.0 (12)
        Potential type of restraints: upper-bound-parabolic (24)
        Total hydrogen bond restraints: upper-bound-parabolic (24)
        O...H-x: upper-bound-parabolic (12)
        O...h-N: upper-bound-parabolic (12)
        Range of distance target values: 2.3, 3.3 (Å)
        Histogram of distance target values
        Distance restraints per residue
        Chain_ID: A
        Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_7
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 33, Sequence coverage: 100.0%
- Total number of restraints: 551
- Total number of restraints per polymer type: 551
- Weight of restraints: 1.0 (551)
- Potential type of restraints: square-well-parabolic (551)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords ANTIMICROBIAL PROTEIN, PROTEIN

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Found 1 Document (0.372 seconds)

BMRB: 34313

Sample

Experiments performed 3 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 8 contents Detail