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BMRB: 19693

2MIT

Solution structure of oxidized dimeric form of human defensin 5

Authors

Ziarek, J.J., Wommack, A.J., Robson, S.A., Wagner, G., Nolan, E.M.

Assembly

oxidized dimeric form of human defensin 5

Entity

1. oxidized dimeric form of human defensin 5 (polymer, Thiol state: all disulfide bound), 32 monomers, 3588.178 × 2 Da Detail

ATCYCRTGRC ATRESLSGVC EISGRLYRLC CR

Total weight

7176.356 Da

Max. entity weight

3588.178 Da

Entity Connection

disulfide 6 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS3:SG	1:CYS31:SG
2	disulfide	sing	1:CYS5:SG	1:CYS20:SG
3	disulfide	sing	1:CYS10:SG	1:CYS30:SG
4	disulfide	sing	1:CYS20:SG	1:CYS5:SG
5	disulfide	sing	1:CYS3:SG	1:CYS31:SG
6	disulfide	sing	1:CYS10:SG	1:CYS30:SG

Source organism

Exptl. method

Refine. method

simulated annealing, molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 94.2 %, Completeness (bb): 92.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	94.2 % (322 of 342)	96.6 % (172 of 178)	93.2 % (123 of 132)	84.4 % (27 of 32)
Backbone	92.2 % (177 of 192)	92.5 % (62 of 67)	94.6 % (88 of 93)	84.4 % (27 of 32)
Sidechain	97.2 % (174 of 179)	99.1 % (110 of 111)	94.1 % (64 of 68)
Aromatic	75.0 % (12 of 16)	100.0 % (8 of 8)	50.0 % (4 of 8)
Methyl	100.0 % (30 of 30)	100.0 % (15 of 15)	100.0 % (15 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	HD5	[U-99% 13C; U-99% 15N]		0.5 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

Protein Blocks Logo

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

Release date

2014-09-07

Citation

Discovery and characterization of a disulfide-locked C(2)-symmetric defensin peptide
Ziarek, J.J., Wommack, A.J., Robson, S.A., Wagner, G., Nolan, E.M.
J. Am. Chem. Soc. (2014), 136, 13494-13497, PubMed 25181039 , DOI 10.1021/ja505957w , Abstract

Related entities 1. oxidized dimeric form of human defensin 5, : 1 : 4 : 10 : 100 entities Detail

Interaction partners 1. oxidized dimeric form of human defensin 5, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 13 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	HD5	[U-99% 13C; U-99% 15N]		0.5 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

2 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	HD5	[U-99% 13C; U-99% 15N]		0.5 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

3 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	HD5	[U-99% 13C; U-99% 15N]		0.5 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

4 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	HD5	[U-99% 13C; U-99% 15N]		0.5 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

5 3D HNCACB

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	HD5	[U-99% 13C; U-99% 15N]		0.5 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

6 3D HCCH-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	HD5	[U-99% 13C; U-99% 15N]		0.5 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

7 3D C(CO)NH

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	HD5	[U-99% 13C; U-99% 15N]		0.5 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

8 3D H(CCO)NH

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	HD5	[U-99% 13C; U-99% 15N]		0.5 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

9 3D HNHB

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	HD5	[U-99% 13C; U-99% 15N]		0.5 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

10 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	HD5	[U-99% 13C; U-99% 15N]		0.5 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

11 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	HD5	[U-99% 13C; U-99% 15N]		0.5 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

12 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, Details Mixed dimer. [U-15N,13-C]-HD5 was mixed with unlabeled-HD5.

#	Name	Isotope labeling	Type	Concentration
4	HD5	[U-99% 13C; U-99% 15N]		0.3 mM
5	HD5	natural abundance		0.3 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

13 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, Details Mixed dimer. [U-15N,13-C]-HD5 was mixed with unlabeled-HD5.

#	Name	Isotope labeling	Type	Concentration
4	HD5	[U-99% 13C; U-99% 15N]		0.3 mM
5	HD5	natural abundance		0.3 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19693_2mit.nef
Input source #2: Coordindates	2mit.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 52.424, CB 47.514 ppm	oxidized, CA 53.018, CB 46.072 ppm	2.03
A:5:CYS:SG	B:120:CYS:SG	oxidized, CA 53.833, CB 41.545 ppm	unknown	2.042
A:10:CYS:SG	A:30:CYS:SG	oxidized, CA 50.246, CB 33.46 ppm	oxidized, CA 50.276, CB 39.605 ppm	2.038
A:20:CYS:SG	B:105:CYS:SG	oxidized, CA 51.297, CB 42.803 ppm	unknown	2.03
B:103:CYS:SG	B:131:CYS:SG	unknown	unknown	2.032
B:110:CYS:SG	B:130:CYS:SG	unknown	unknown	2.049

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

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

-------110-------120-------130--
ATCYCRTGRCATRESLSGVCEISGRLYRLCCR
||||||||||||||||||||||||||||||||
ATCYCRTGRCATRESLSGVCEISGRLYRLCCR
--------10--------20--------30--

Chain assignments

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

Content subtype: combined_19693_2mit.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	6		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	316		100.0 (chain: A, length: 32)
1	Distance restraints	DYANA/DIANA_distance_constraints_4	OK	1275 (1)	noe	93.8 (chain: A, length: 32), 93.8 (chain: B, length: 32)
2	Distance restraints	DYANA/DIANA_distance_constraints_5	Warning	18 (1)	undefined	18.8 (chain: A, length: 32), 18.8 (chain: B, length: 32)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	82 (82)	.	87.5 (chain: A, length: 32), 87.5 (chain: B, 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: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 167
  - ¹³C chemical shifts: 118
  - ¹⁵N chemical shifts: 31
- 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: DYANA/DIANA_distance_constraints_4
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 32, Sequence coverage: 93.8%
  - Entity_assembly_ID: B, Chain length: 32, Sequence coverage: 93.8%
- Total number of restraints: 1275
- Weight of restraints: 1.0 (1275)
- Potential type of restraints: upper-bound-parabolic (1275)
- Range of distance target values: 2.4, 5.5 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map
- Saveframe: DYANA/DIANA_distance_constraints_5
  - Status: Warning
  - Experiment type: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 32, Sequence coverage: 18.8%
    - Entity_assembly_ID: B, Chain length: 32, Sequence coverage: 18.8%
  - Total number of restraints: 18
  - Weight of restraints: 1.0 (18)
  - Potential type of restraints: upper-bound-parabolic (18)
  - Range of distance target values: 2.1, 3.15 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 32, Sequence coverage: 87.5%
  - Entity_assembly_ID: B, Chain length: 32, Sequence coverage: 87.5%
- Total number of restraints: 82
- Total number of restraints per polymer type: 82
- Weight of restraints: 1.0 (82)
- Potential type of restraints: square-well-parabolic (82)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

Keywords antimicrobial peptide, cysteine knot, human defensin 5, solution NMR