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BMRB: 16665

2KSI

Solution NMR structure of Sterol Carrier Protein - 2 from Aedes aegypti (AeSCP-2) complex with C16 fatty acid (palmitate)

Authors

Singarapu, K., Radek, J.T., Tonelli, M., Lan, Q., Markley, J.L.

Assembly

AeSCP-2-PA

Entity

1. AeSCP-2-PA (polymer, Thiol state: all free), 110 monomers, 12272.10 Da Detail

MSLKSDEVFA KIAKRLESID PANRQVEHVY KFRITQGGKV VKNWVMDLKN VKLVESDDAA EATLTMEDDI MFAIGTGALP AKEAMAQDKM EVDGQVELIF LLEPFIASLK

2. PALMITIC ACID (non-polymer), 256.424 Da

Total weight

12528.523 Da

Max. entity weight

12272.1 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts, RDCs

Chem. Shift Complete

Sequence coverage: 99.1 %, Completeness: 87.3 %, Completeness (bb): 83.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	87.3 % (1129 of 1293)	93.0 % (624 of 671)	77.5 % (393 of 507)	97.4 % (112 of 115)
Backbone	83.5 % (546 of 654)	94.6 % (210 of 222)	71.1 % (231 of 325)	98.1 % (105 of 107)
Sidechain	92.2 % (686 of 744)	92.2 % (414 of 449)	92.3 % (265 of 287)	87.5 % (7 of 8)
Aromatic	82.4 % (61 of 74)	100.0 % (37 of 37)	66.7 % (24 of 36)	0.0 % (0 of 1)
Methyl	97.9 % (137 of 140)	97.1 % (68 of 70)	98.6 % (69 of 70)

1. AeSCP-2-PA

MSLKSDEVFA KIAKRLESID PANRQVEHVY KFRITQGGKV VKNWVMDLKN VKLVESDDAA EATLTMEDDI MFAIGTGALP AKEAMAQDKM EVDGQVELIF LLEPFIASLK

Show sample condition

Sample #1

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
1	AeSCP-2-PA	[U-100% 13C; U-100% 15N]		2 mM
2	AeSCP-2-PA	[U-100% 15N]		1 mM

Sample #2

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
3	AeSCP-2-PA	[U-100% 15N]		2 mM

Sample #3

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
4	AeSCP-2-PA	[U-100% 15N]		2 mM

Protein Blocks Logo

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

RDC

92 RDC values in 1 lists
Field strength (¹H) 600 MHz, Pressure 1 atm, Temperature 298 K, pH 7.8 Detail

Release date

2010-05-04

Citation

Differences in the structure and dynamics of the apo- and palmitate-ligated forms of Aedes aegypti sterol carrier protein 2 (AeSCP-2)
Singarapu, K.K., Radek, J.T., Tonelli, M., Markley, J.L., Lan, Q.
J. Biol. Chem. (2010), 285, 17046-17053, PubMed 20356842 , DOI 10.1074/jbc.M110.101154 , Abstract

Related entities 1. AeSCP-2-PA, : 15 entities Detail

Experiments performed 14 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
1	AeSCP-2-PA	[U-100% 13C; U-100% 15N]		2 mM
2	AeSCP-2-PA	[U-100% 15N]		1 mM

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
1	AeSCP-2-PA	[U-100% 13C; U-100% 15N]		2 mM
2	AeSCP-2-PA	[U-100% 15N]		1 mM

3 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
1	AeSCP-2-PA	[U-100% 13C; U-100% 15N]		2 mM
2	AeSCP-2-PA	[U-100% 15N]		1 mM

4 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
1	AeSCP-2-PA	[U-100% 13C; U-100% 15N]		2 mM
2	AeSCP-2-PA	[U-100% 15N]		1 mM

5 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
1	AeSCP-2-PA	[U-100% 13C; U-100% 15N]		2 mM
2	AeSCP-2-PA	[U-100% 15N]		1 mM

6 3D H(CCO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
1	AeSCP-2-PA	[U-100% 13C; U-100% 15N]		2 mM
2	AeSCP-2-PA	[U-100% 15N]		1 mM

7 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
1	AeSCP-2-PA	[U-100% 13C; U-100% 15N]		2 mM
2	AeSCP-2-PA	[U-100% 15N]		1 mM

8 3D 1H-13C NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
1	AeSCP-2-PA	[U-100% 13C; U-100% 15N]		2 mM
2	AeSCP-2-PA	[U-100% 15N]		1 mM

9 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
1	AeSCP-2-PA	[U-100% 13C; U-100% 15N]		2 mM
2	AeSCP-2-PA	[U-100% 15N]		1 mM

10 15N,13C filtered 1H-13C NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
1	AeSCP-2-PA	[U-100% 13C; U-100% 15N]		2 mM
2	AeSCP-2-PA	[U-100% 15N]		1 mM

11 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
3	AeSCP-2-PA	[U-100% 15N]		2 mM

12 2D 1H-15N TROSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
3	AeSCP-2-PA	[U-100% 15N]		2 mM

13 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
4	AeSCP-2-PA	[U-100% 15N]		2 mM

14 2D 1H-15N TROSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
4	AeSCP-2-PA	[U-100% 15N]		2 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_16665_2ksi.nef
Input source #2: Coordindates	2ksi.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	Assigned chemical shifts, Distance restraints

Sequence alignments

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

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

-------110
LLEPFIASLK
||||||||||
LLEPFIASLK

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	110	0	0	100.0

Content subtype: combined_16665_2ksi.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1162		99.1 (chain: A, length: 110), 100.0 (chain: B, length: 1)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	2417 (1)	noe	99.1 (chain: A, length: 110), 100.0 (chain: B, length: 1)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_4	Warning	437 (430)	.	100.0 (chain: A, length: 110)
1	RDC restraints	DYANA/DIANA_dipolar_coupling_2	OK	92 (92)	.	83.6 (chain: A, length: 110)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 110, Sequence coverage: 99.1%
  - Entity_assembly_ID: B, Chain length: 1, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 674
  - ¹³C chemical shifts: 376
  - ¹⁵N chemical shifts: 112
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- 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_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 110, Sequence coverage: 99.1%
  - Entity_assembly_ID: B, Chain length: 1, Sequence coverage: 100.0%
- Total number of restraints: 2417
- Weight of restraints: 1.0 (2417)
- Potential type of restraints: upper-bound-parabolic (2417)
- Range of distance target values: 2.4, 11.14 (Å)
- Histogram of distance target values
- Histogram of discrepancy in 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_4
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 110, Sequence coverage: 100.0%
- Total number of restraints: 430
- Total number of restraints per polymer type: 430
- Weight of restraints: 1.0 (430)
- Potential type of restraints: square-well-parabolic (430)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: DYANA/DIANA_dipolar_coupling_2

Status: OK
Experiment type: .

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 110, Sequence coverage: 83.6%

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
MSLKSDEVFAKIAKRLESIDPANRQVEHVYKFRITQGGKVVKNWVMDLKNVKLVESDDAAEATLTMEDDIMFAIGTGALPAKEAMAQDKMEVDGQVELIF
  ||||||||||||||   |     |   ||||| ||||||||||||||||| |||||||||||||||||||||||||| |||||||||||||| |||||
..LKSDEVFAKIAKRL...D.....V...YKFRI.QGGKVVKNWVMDLKNVK.VESDDAAEATLTMEDDIMFAIGTGAL.AKEAMAQDKMEVDG.VELIF

-------110
LLEPFIASLK
||| ||||||
LLE.FIASLK

Total number of restraints: 92
Potential type of restraints: undefined (92)
Range of observed RDC values: 100.0, -100.0 (Hz)
RDC restraints per residue
- Chain_ID: A
  None