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BMRB: 18705

2LXZ

Solution Structure of the Antimicrobial Peptide Human Defensin 5

Authors

Wommack, A.J., Robson, S.A., Wanniarahchi, Y.A., Wan, A., Turner, C.J., Nolan, E.M.

Assembly

Antimicrobial Peptide Human Defensin 5

Entity

1. Antimicrobial Peptide Human Defensin 5 (polymer), 32 monomers, 3588.178 Da Detail

ATCYCRTGRC ATRESLSGVC EISGRLYRLC CR

Formula weight

3588.178 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 93.8 %, Completeness: 80.4 %, Completeness (bb): 83.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	80.4 % (275 of 342)	84.8 % (151 of 178)	73.5 % (97 of 132)	84.4 % (27 of 32)
Backbone	83.3 % (160 of 192)	89.6 % (60 of 67)	78.5 % (73 of 93)	84.4 % (27 of 32)
Sidechain	79.3 % (142 of 179)	82.0 % (91 of 111)	75.0 % (51 of 68)
Aromatic	50.0 % (8 of 16)	100.0 % (8 of 8)	0.0 % (0 of 8)
Methyl	90.0 % (27 of 30)	100.0 % (15 of 15)	80.0 % (12 of 15)

1. entity

ATCYCRTGRC ATRESLSGVC EISGRLYRLC CR

Show sample condition

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	TFA	natural abundance		0.0 ~ 1.0 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

Protein Blocks Logo

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

Release date

2012-11-26

Citation

NMR solution structure and condition-dependent oligomerization of the antimicrobial peptide human defensin 5
Wommack, A.J., Robson, S.A., Wanniarachchi, Y.A., Wan, A., Turner, C.J., Wagner, G., Nolan, E.M.
Biochemistry (2012), 51, 9624-9637, PubMed 23163963 , DOI 10.1021/bi301255u , Abstract

Related entities 1. Antimicrobial Peptide Human Defensin 5, : 1 : 4 : 10 : 100 entities Detail

Interaction partners 1. Antimicrobial Peptide Human Defensin 5, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 8 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	TFA	natural abundance		0.0 ~ 1.0 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

2 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	TFA	natural abundance		0.0 ~ 1.0 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

3 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	TFA	natural abundance		0.0 ~ 1.0 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

4 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	TFA	natural abundance		0.0 ~ 1.0 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

5 3D HNCA

Instrument

Bruker Avance - 600 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	TFA	natural abundance		0.0 ~ 1.0 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

6 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	TFA	natural abundance		0.0 ~ 1.0 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

7 3D 1H-13C NOESY

Instrument

Bruker Avance - 600 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	TFA	natural abundance		0.0 ~ 1.0 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

8 3D HCACO

Instrument

Bruker Avance - 600 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	TFA	natural abundance		0.0 ~ 1.0 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18705_2lxz.nef
Input source #2: Coordindates	2lxz.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:3:CYS:SG	A:31:CYS:SG	oxidized, CA 55.069, CB 49.718 ppm	oxidized, CA 55.684, CB 49.066 ppm	2.016
A:5:CYS:SG	A:20:CYS:SG	oxidized, CA 56.553, CB 42.208 ppm	oxidized, CA 54.476, CB 43.178 ppm	2.018
A:10:CYS:SG	A:30:CYS:SG	oxidized, CA 52.737, CB 35.343 ppm	oxidized, CA 53.458, CB 43.152 ppm	2.018

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--
ATCYCRTGRCATRESLSGVCEISGRLYRLCCR
||||||||||||||||||||||||||||||||
ATCYCRTGRCATRESLSGVCEISGRLYRLCCR

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	32	0	0	100.0

Content subtype: combined_18705_2lxz.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	3		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	274		93.8 (chain: A, length: 32)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	637 (1)	noe	100.0 (chain: A, length: 32)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	70 (70)	.	100.0 (chain: A, length: 32)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 32, Sequence coverage: 93.8%
- Total number of assignments
  - ¹H chemical shifts: 151
  - ¹³C chemical shifts: 96
  - ¹⁵N chemical shifts: 27
- 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: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 32, Sequence coverage: 100.0%
- Total number of restraints: 626
- Weight of restraints: 1.0 (626)
- Potential type of restraints: square-well-parabolic (626)
- Range of distance target values: 1.17, 3.25 (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

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 32, Sequence coverage: 100.0%
- Total number of restraints: 70
- Total number of restraints per polymer type: 70
- Weight of restraints: 1.0 (70)
- Potential type of restraints: square-well-parabolic (70)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Cysteine Knot, Human Defensin 5