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Found 1 Document (1.366 seconds)

BMRB: 25605

2N2Q

NMR solution structure of HsAFP1

Authors

Harvey, P.J., Craik, D.J., Vriens, K.

Assembly

HsAFP1

Entity

1. HsAFP1 (polymer, Thiol state: all disulfide bound), 54 monomers, 5948.667 Da Detail

DGVKLCDVPS GTWSGHCGSS SKCSQQCKDR EHFAYGGACH YQFPSVKCFC KRQC

Formula weight

5948.667 Da

Entity Connection

disulfide 4 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS6:SG	1:CYS54:SG
2	disulfide	sing	1:CYS17:SG	1:CYS39:SG
3	disulfide	sing	1:CYS23:SG	1:CYS48:SG
4	disulfide	sing	1:CYS27:SG	1:CYS50:SG

Source organism

Heuchera sanguinea

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.1 %, Completeness: 73.1 %, Completeness (bb): 61.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	73.1 % (437 of 598)	94.9 % (297 of 313)	44.3 % (101 of 228)	68.4 % (39 of 57)
Backbone	61.9 % (198 of 320)	96.4 % (108 of 112)	34.0 % (53 of 156)	71.2 % (37 of 52)
Sidechain	78.5 % (256 of 326)	90.5 % (182 of 201)	60.0 % (72 of 120)	40.0 % (2 of 5)
Aromatic	78.6 % (55 of 70)	85.7 % (30 of 35)	73.5 % (25 of 34)	0.0 % (0 of 1)
Methyl	90.9 % (20 of 22)	100.0 % (11 of 11)	81.8 % (9 of 11)

1. entity

DGVKLCDVPS GTWSGHCGSS SKCSQQCKDR EHFAYGGACH YQFPSVKCFC KRQC

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	entity	natural abundance	protein	1 mM
2	H2O	natural abundance	solvent	90 %
3	D2O	[U-2H]	solvent	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 4 (±0.1)

#	Name	Isotope labeling	Type	Concentration
4	entity	natural abundance	protein	1 mM
5	D2O	[U-2H]	solvent	100 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2N2Q, Strand ID: A Detail

Release date

2015-07-19

Citation

Synergistic Activity of the Plant Defensin HsAFP1 and Caspofungin against Candida albicans Biofilms and Planktonic Cultures
Vriens, K., Cools, T.L., Harvey, P.J., Craik, D.J., Spincemaille, P., Cassiman, D., Braem, A., Vleugels, J., Nibbering, P.H., Drijfhout, J.WOUTER., Coninck, B.DE., Cammue, B.P.A., Thevissen, K.
PLoS One (2015), 10, e0132701-e0132701, PubMed 26248029 , DOI 10.1371/journal.pone.0132701 , Abstract

Related entities 1. HsAFP1, : 1 : 1 : 63 entities Detail

Experiments performed 5 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25605_2n2q.nef
Input source #2: Coordindates	2n2q.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:54:CYS:SG	unknown, CA 58.402 ppm	unknown	2.025
A:17:CYS:SG	A:39:CYS:SG	unknown, CA 55.028 ppm	unknown, CA 52.231 ppm	2.045
A:23:CYS:SG	A:48:CYS:SG	unknown, CA 61.269 ppm	unknown	2.024
A:27:CYS:SG	A:50:CYS:SG	unknown	unknown, CA 51.653 ppm	2.029

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--------40--------50----
DGVKLCDVPSGTWSGHCGSSSKCSQQCKDREHFAYGGACHYQFPSVKCFCKRQC
||||||||||||||||||||||||||||||||||||||||||||||||||||||
DGVKLCDVPSGTWSGHCGSSSKCSQQCKDREHFAYGGACHYQFPSVKCFCKRQC

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	54	0	0	100.0

Content subtype: combined_25605_2n2q.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	453		98.1 (chain: A, length: 54)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	843 (1)	noe	98.1 (chain: A, length: 54)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	30 (1)	hbond	40.7 (chain: A, length: 54)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	88 (88)	.	96.3 (chain: A, length: 54)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 54, Sequence coverage: 98.1%
- Total number of assignments
  - ¹H chemical shifts: 315
  - ¹³C chemical shifts: 99
  - ¹⁵N chemical shifts: 39
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
4	LYS	HZ1	7.487
4	LYS	HZ2	7.487
4	LYS	HZ3	7.487
22	LYS	HZ1	7.597
22	LYS	HZ2	7.597
22	LYS	HZ3	7.597
28	LYS	HZ1	7.543
28	LYS	HZ2	7.543
28	LYS	HZ3	7.543
51	LYS	HZ1	7.548
51	LYS	HZ2	7.548
51	LYS	HZ3	7.548

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	313	303	96.8
¹³C chemical shifts	228	99	43.4
¹⁵N chemical shifts	59	39	66.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	112	110	98.2
¹³C chemical shifts	108	28	25.9
¹⁵N chemical shifts	52	37	71.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	201	193	96.0
¹³C chemical shifts	120	71	59.2
¹⁵N chemical shifts	7	2	28.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	11	11	100.0
¹³C chemical shifts	11	9	81.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	35	30	85.7
¹³C chemical shifts	34	25	73.5
¹⁵N chemical shifts	1	0	0.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 54, Sequence coverage: 98.1%
- Total number of restraints: 839
- Weight of restraints: 1.0 (839)
- Potential type of restraints: square-well-parabolic (839)
- Range of distance target values: 2.27, 3.77 (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
- Saveframe: CNS/XPLOR_distance_constraints_4
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 54, Sequence coverage: 40.7%
  - Total number of restraints: 30
  - Weight of restraints: 1.0 (30)
  - Potential type of restraints: square-well-parabolic (30)
  - Range of distance target values: 1.0, 1.5 (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_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 54, Sequence coverage: 96.3%
- Total number of restraints: 88
- Total number of restraints per polymer type: 88
- Weight of restraints: 1.0 (88)
- Potential type of restraints: square-well-parabolic (88)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords peptide

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Found 1 Document (1.366 seconds)

BMRB: 25605

Sample #1

Sample #2

Related entities 1. HsAFP1, : 1 : 1 : 63 entities Detail

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail