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BMRB: 19660

2MHY

Structure determination of the salamander courtship pheromone Plethodontid Modulating Factor

Authors

Wilburn, D.B., Bowen, K.E., Doty, K.A., Arumugam, S., Lane, A.N., Feldhoff, P.W., Feldhoff, R.C.

Assembly

pmf-g

Entity

1. pmf-g (polymer, Thiol state: all disulfide bound), 57 monomers, 6264.820 Da Detail

LQCNTLDGGT EECIPGIYNV CVHYKSEDEE YKSCGIQEEC EDAEGATVLC CPEDLCN

Formula weight

6264.82 Da

Source organism

Plethodon shermani

Exptl. method

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts, H_exch_rates

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 88.4 %, Completeness (bb): 86.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	88.4 % (533 of 603)	98.4 % (306 of 311)	73.7 % (171 of 232)	93.3 % (56 of 60)
Backbone	86.7 % (293 of 338)	97.4 % (114 of 117)	77.1 % (128 of 166)	92.7 % (51 of 55)
Sidechain	90.2 % (286 of 317)	99.0 % (192 of 194)	75.4 % (89 of 118)	100.0 % (5 of 5)
Aromatic	78.6 % (22 of 28)	100.0 % (14 of 14)	57.1 % (8 of 14)
Methyl	84.0 % (42 of 50)	100.0 % (25 of 25)	68.0 % (17 of 25)

1. rPMF-G

LQCNTLDGGT EECIPGIYNV CVHYKSEDEE YKSCGIQEEC EDAEGATVLC CPEDLCN

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7, Details 50 mM KCl, 10mM NaPO4 pH 7

#	Name	Isotope labeling	Type	Concentration
1	rPMF-G	[U-98% 15N]		2.2 mM
2	KCl	natural abundance		50 mM
3	NaPO4	natural abundance		10 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

Protein Blocks Logo

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

¹H exchange rate

57 k_ex values in 1 lists
Pressure 1 atm, Temperature 293 K, pH 7 Detail

Release date

2014-01-01

Citation

Structural insights into the evolution of a sexy protein: novel topology and restricted backbone flexibility in a hypervariable pheromone from the red-legged salamander, Plethodon shermani
Wilburn, D.B., Bowen, K.E., Doty, K.A., Arumugam, S., Lane, A.N., Feldhoff, P.W., Feldhoff, R.C.
PLoS One (2014), 9, e96975-e96975, PubMed 24849290 , DOI 10.1371/journal.pone.0096975 , Abstract

Related entities 1. pmf-g, : 1 : 2 entities Detail

Experiments performed 8 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7, Details 50 mM KCl, 10mM NaPO4 pH 7

#	Name	Isotope labeling	Type	Concentration
1	rPMF-G	[U-98% 15N]		2.2 mM
2	KCl	natural abundance		50 mM
3	NaPO4	natural abundance		10 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

2 2D 1H-1H NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7, Details 50 mM KCl, 10mM NaPO4 pH 7

#	Name	Isotope labeling	Type	Concentration
1	rPMF-G	[U-98% 15N]		2.2 mM
2	KCl	natural abundance		50 mM
3	NaPO4	natural abundance		10 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

3 3D HNCO

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7, Details 50 mM KCl, 10mM NaPO4 pH 7

#	Name	Isotope labeling	Type	Concentration
1	rPMF-G	[U-98% 15N]		2.2 mM
2	KCl	natural abundance		50 mM
3	NaPO4	natural abundance		10 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

4 3D 1H-15N NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7, Details 50 mM KCl, 10mM NaPO4 pH 7

#	Name	Isotope labeling	Type	Concentration
1	rPMF-G	[U-98% 15N]		2.2 mM
2	KCl	natural abundance		50 mM
3	NaPO4	natural abundance		10 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

5 3D 1H-15N TOCSY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7, Details 50 mM KCl, 10mM NaPO4 pH 7

#	Name	Isotope labeling	Type	Concentration
1	rPMF-G	[U-98% 15N]		2.2 mM
2	KCl	natural abundance		50 mM
3	NaPO4	natural abundance		10 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

6 2D 1H-13C HSQC

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7, Details 50 mM KCl, 10mM NaPO4 pH 7

#	Name	Isotope labeling	Type	Concentration
1	rPMF-G	[U-98% 15N]		2.2 mM
2	KCl	natural abundance		50 mM
3	NaPO4	natural abundance		10 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

7 2D 1H-1H TOCSY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7, Details 50 mM KCl, 10mM NaPO4 pH 7

#	Name	Isotope labeling	Type	Concentration
1	rPMF-G	[U-98% 15N]		2.2 mM
2	KCl	natural abundance		50 mM
3	NaPO4	natural abundance		10 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

8 2D 1H-1H COSY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7, Details 50 mM KCl, 10mM NaPO4 pH 7

#	Name	Isotope labeling	Type	Concentration
1	rPMF-G	[U-98% 15N]		2.2 mM
2	KCl	natural abundance		50 mM
3	NaPO4	natural abundance		10 mM
4	H2O	natural abundance		90 %
5	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_19660_2mhy.nef
Input source #2: Coordindates	2mhy.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:13:CYS:SG	unknown, CA 51.967 ppm	oxidized, CA 52.626, CB 37.284 ppm	2.106
A:21:CYS:SG	A:50:CYS:SG	oxidized, CA 52.5, CB 38.42 ppm	oxidized, CA 54.289, CB 46.424 ppm	1.852

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-------
LQCNTLDGGTEECIPGIYNVCVHYKSEDEEYKSCGIQEECEDAEGATVLCCPEDLCN
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LQCNTLDGGTEECIPGIYNVCVHYKSEDEEYKSCGIQEECEDAEGATVLCCPEDLCN

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	57	0	0	100.0

Content subtype: combined_19660_2mhy.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	2		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	529		100.0 (chain: A, length: 57)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	916 (1)	noe	98.2 (chain: A, length: 57)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	76 (76)	.	91.2 (chain: A, length: 57)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 57, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 302
  - ¹³C chemical shifts: 171
  - ¹⁵N chemical shifts: 56
- 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

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 57, Sequence coverage: 98.2%
- Total number of restraints: 916
- Weight of restraints: 1.0 (916)
- Potential type of restraints: upper-bound-parabolic (916)
- Range of distance target values: 2.0, 5.5 (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: DYANA/DIANA_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 57, Sequence coverage: 91.2%
- Total number of restraints: 76
- Total number of restraints per polymer type: 76
- Weight of restraints: 1.0 (76)
- Potential type of restraints: square-well-parabolic (76)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords pheromone, PMF, salamander, TFP, three-finger protein