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BMRB: 25984

2NBN

Solution NMR structure of palmitated SCP2L2 from Aedes aegypti

Authors

Singarapu, K.K., Ummanni, R.

Assembly

palmitated SCP2L2

Entity

1. palmitated SCP2L2, entity 1 (polymer, Thiol state: not present), 111 monomers, 11922.61 Da Detail

MSVETIIERI KARVGAVDPN GPRKVLGVFQ LNIKTASGVE QWIVDLKQLK VDQGVFASPD VTVTVGLEDM LAISGKTLTV GDALKQGKIE LSGDADLAAK LAEVIHHHHH H

2. PALMITOLEIC ACID (non-polymer), 254.408 × 2 Da

Total weight

12431.427 Da

Max. entity weight

11922.61 Da

Source organism

Exptl. method

Refine. method

DGSA-distance geometry simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.4 %, Completeness: 86.4 %, Completeness (bb): 82.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	86.4 % (1084 of 1254)	92.7 % (596 of 643)	76.0 % (376 of 495)	96.6 % (112 of 116)
Backbone	82.1 % (542 of 660)	96.1 % (220 of 229)	67.5 % (218 of 323)	96.3 % (104 of 108)
Sidechain	91.8 % (638 of 695)	90.8 % (376 of 414)	93.0 % (254 of 273)	100.0 % (8 of 8)
Aromatic	66.1 % (37 of 56)	71.4 % (20 of 28)	59.3 % (16 of 27)	100.0 % (1 of 1)
Methyl	98.8 % (162 of 164)	98.8 % (81 of 82)	98.8 % (81 of 82)

1. entity 1

MSVETIIERI KARVGAVDPN GPRKVLGVFQ LNIKTASGVE QWIVDLKQLK VDQGVFASPD VTVTVGLEDM LAISGKTLTV GDALKQGKIE LSGDADLAAK LAEVIHHHHH H

Show sample condition

Sample #1

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 15N]	protein	1.0 mM
2	PALMITOLEIC ACID	natural abundance		2.0 mM
3	H2O	natural abundance	solvent	93 %
4	D2O	[U-2H]	solvent	7 %

Sample #2

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
5	entity_1	[U-100% 13C; U-100% 15N]	protein	1.0 mM
6	PALMITOLEIC ACID	natural abundance		2.0 mM
7	H2O	natural abundance	solvent	93 %
8	D2O	[U-2H]	solvent	7 %

Protein Blocks Logo

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

Release date

2016-03-16

Citation

Solution Nuclear Magnetic Resonance Studies of Sterol Carrier Protein 2 Like 2 (SCP2L2) Reveal the Insecticide Specific Structural Characteristics of SCP2 Proteins in Aedes aegypti Mosquitoes
Singarapu, K.K., Ahuja, A., Potula, P.R., Ummanni, R.
Biochemistry (2016), 55, 4919-4927, PubMed 27508310 , DOI 10.1021/acs.biochem.6b00322 , Abstract

Related entities 1. palmitated SCP2L2, entity 1, : 1 : 1 : 2 : 25 entities Detail

Experiments performed 8 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 15N]	protein	1.0 mM
2	PALMITOLEIC ACID	natural abundance		2.0 mM
3	H2O	natural abundance	solvent	93 %
4	D2O	[U-2H]	solvent	7 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
5	entity_1	[U-100% 13C; U-100% 15N]	protein	1.0 mM
6	PALMITOLEIC ACID	natural abundance		2.0 mM
7	H2O	natural abundance	solvent	93 %
8	D2O	[U-2H]	solvent	7 %

3 3D CBCA(CO)NH

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
5	entity_1	[U-100% 13C; U-100% 15N]	protein	1.0 mM
6	PALMITOLEIC ACID	natural abundance		2.0 mM
7	H2O	natural abundance	solvent	93 %
8	D2O	[U-2H]	solvent	7 %

4 3D HNCACB

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
5	entity_1	[U-100% 13C; U-100% 15N]	protein	1.0 mM
6	PALMITOLEIC ACID	natural abundance		2.0 mM
7	H2O	natural abundance	solvent	93 %
8	D2O	[U-2H]	solvent	7 %

5 3D HBHA(CO)NH

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
5	entity_1	[U-100% 13C; U-100% 15N]	protein	1.0 mM
6	PALMITOLEIC ACID	natural abundance		2.0 mM
7	H2O	natural abundance	solvent	93 %
8	D2O	[U-2H]	solvent	7 %

6 3D HCCH-COSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
5	entity_1	[U-100% 13C; U-100% 15N]	protein	1.0 mM
6	PALMITOLEIC ACID	natural abundance		2.0 mM
7	H2O	natural abundance	solvent	93 %
8	D2O	[U-2H]	solvent	7 %

7 3D 1H-15N NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
5	entity_1	[U-100% 13C; U-100% 15N]	protein	1.0 mM
6	PALMITOLEIC ACID	natural abundance		2.0 mM
7	H2O	natural abundance	solvent	93 %
8	D2O	[U-2H]	solvent	7 %

8 3D 1H-13C NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
5	entity_1	[U-100% 13C; U-100% 15N]	protein	1.0 mM
6	PALMITOLEIC ACID	natural abundance		2.0 mM
7	H2O	natural abundance	solvent	93 %
8	D2O	[U-2H]	solvent	7 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25984_2nbn.nef
Input source #2: Coordindates	2nbn.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	PLM	PALMITIC ACID	None
B	2	PLM	PALMITIC ACID	None
B	201	PAM	PALMITOLEIC ACID	Assigned chemical shifts

Sequence alignments

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

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
MSVETIIERIKARVGAVDPNGPRKVLGVFQLNIKTASGVEQWIVDLKQLKVDQGVFASPDVTVTVGLEDMLAISGKTLTVGDALKQGKIELSGDADLAAK
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MSVETIIERIKARVGAVDPNGPRKVLGVFQLNIKTASGVEQWIVDLKQLKVDQGVFASPDVTVTVGLEDMLAISGKTLTVGDALKQGKIELSGDADLAAK

-------110-
LAEVIHHHHHH
|||||||||||
LAEVIHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	111	0	0	100.0

Content subtype: combined_25984_2nbn.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1079		94.6 (chain: A, length: 111), 33.3 (chain: B, length: 3)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	2527 (1)	noe	94.6 (chain: A, length: 111)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	Warning	431 (428)	.	95.5 (chain: A, length: 111)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 111, Sequence coverage: 94.6%
  - Entity_assembly_ID: B, Chain length: 3, Sequence coverage: 33.3%
- Total number of assignments
  - ¹H chemical shifts: 615
  - ¹³C chemical shifts: 354
  - ¹⁵N chemical shifts: 110
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 111, Sequence coverage: 94.6%
- Total number of restraints: 2527
- Weight of restraints: 1.0 (2527)
- Potential type of restraints: upper-bound-parabolic (2527)
- Range of distance target values: 2.19, 5.94 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_3
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 111, Sequence coverage: 95.5%
- Total number of restraints: 428
- Total number of restraints per polymer type: 428
- Weight of restraints: 1.0 (428)
- Potential type of restraints: square-well-parabolic (428)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Aedes aegypti, Palmitate, SCP2L2, Solution NMR