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Found 1 Document (0.589 seconds)

BMRB: 25609

2N2R

NMR solution structure of RsAFP2

Authors

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

Assembly

RsAFP2

Entity

1. RsAFP2 (polymer, Thiol state: all disulfide bound), 51 monomers, 5735.611 Da Detail

QKLCQRPSGT WSGVCGNNNA CKNQCIRLEK ARHGSCNYVF PAHKCICYFP C

Formula weight

5735.611 Da

Entity Connection

disulfide 4 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS4:SG	1:CYS51:SG
2	disulfide	sing	1:CYS15:SG	1:CYS36:SG
3	disulfide	sing	1:CYS21:SG	1:CYS45:SG
4	disulfide	sing	1:CYS25:SG	1:CYS47:SG

Source organism

Raphanus sativus

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 86.4 %, Completeness (bb): 77.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	86.4 % (509 of 589)	98.4 % (306 of 311)	68.3 % (151 of 221)	91.2 % (52 of 57)
Backbone	77.7 % (233 of 300)	99.0 % (102 of 103)	58.4 % (87 of 149)	91.7 % (44 of 48)
Sidechain	92.9 % (312 of 336)	98.1 % (204 of 208)	84.0 % (100 of 119)	88.9 % (8 of 9)
Aromatic	92.9 % (52 of 56)	92.9 % (26 of 28)	92.6 % (25 of 27)	100.0 % (1 of 1)
Methyl	96.9 % (31 of 32)	100.0 % (16 of 16)	93.8 % (15 of 16)

1. entity

QKLCQRPSGT WSGVCGNNNA CKNQCIRLEK ARHGSCNYVF PAHKCICYFP C

Show sample condition

Sample #1

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

#	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

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

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.39 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.39 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.04 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2N2R, Strand ID: A Detail

Release date

2016-05-22

Citation

The radish defensins RsAFP1 and RsAFP2 act synergistically with caspofungin against Candida albicans biofilms
Vriens, K., Cools, T.L., Harvey, P.J., Craik, D.J., DeConinck, B., Cammue, B.PA., Thevissen, K.
Peptides (2015), 75, 71-79, PubMed 26592804 , DOI 10.1016/j.peptides.2015.11.001 , Abstract

Related entities 1. RsAFP2, : 1 : 1 : 75 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_25609_2n2r.nef
Input source #2: Coordindates	2n2r.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:4:CYS:SG	A:51:CYS:SG	oxidized, CA 59.422, CB 39.243 ppm	unknown, CA 56.585 ppm	2.03
A:15:CYS:SG	A:36:CYS:SG	unknown, CA 56.967 ppm	oxidized, CA 51.982, CB 36.289 ppm	2.01
A:21:CYS:SG	A:45:CYS:SG	oxidized, CA 58.18, CB 36.91 ppm	oxidized, CB 35.576 ppm	2.027
A:25:CYS:SG	A:47:CYS:SG	oxidized, CA 57.322, CB 36.914 ppm	unknown, CA 51.196 ppm	2.032

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-
QKLCQRPSGTWSGVCGNNNACKNQCIRLEKARHGSCNYVFPAHKCICYFPC
|||||||||||||||||||||||||||||||||||||||||||||||||||
QKLCQRPSGTWSGVCGNNNACKNQCIRLEKARHGSCNYVFPAHKCICYFPC

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	51	0	0	100.0

Content subtype: combined_25609_2n2r.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	508		100.0 (chain: A, length: 51)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	872 (1)	noe	100.0 (chain: A, length: 51)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	34 (1)	hbond	47.1 (chain: A, length: 51)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	90 (90)	.	100.0 (chain: A, length: 51)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 51, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 315
  - ¹³C chemical shifts: 142
  - ¹⁵N chemical shifts: 51
- 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)
2	LYS	HZ1	7.546
2	LYS	HZ2	7.546
2	LYS	HZ3	7.546
30	LYS	HZ1	7.553
30	LYS	HZ2	7.553
30	LYS	HZ3	7.553
44	LYS	HZ1	7.651
44	LYS	HZ2	7.651
44	LYS	HZ3	7.651

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	311	306	98.4
¹³C chemical shifts	221	142	64.3
¹⁵N chemical shifts	60	51	85.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	103	102	99.0
¹³C chemical shifts	102	44	43.1
¹⁵N chemical shifts	48	43	89.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	208	204	98.1
¹³C chemical shifts	119	98	82.4
¹⁵N chemical shifts	12	8	66.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	16	16	100.0
¹³C chemical shifts	16	15	93.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	28	26	92.9
¹³C chemical shifts	27	25	92.6
¹⁵N chemical shifts	1	1	100.0

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: 51, Sequence coverage: 100.0%
- Total number of restraints: 872
- Weight of restraints: 1.0 (872)
- Potential type of restraints: square-well-parabolic (872)
- Range of distance target values: 2.07, 3.65 (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: 51, Sequence coverage: 47.1%
  - Total number of restraints: 34
  - Weight of restraints: 1.0 (34)
  - Potential type of restraints: square-well-parabolic (34)
  - 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: 51, Sequence coverage: 100.0%
- Total number of restraints: 90
- Total number of restraints per polymer type: 90
- Weight of restraints: 1.0 (90)
- Potential type of restraints: square-well-parabolic (90)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords protein

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Found 1 Document (0.589 seconds)

BMRB: 25609

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. RsAFP2, : 1 : 1 : 75 entities Detail

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail