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Found 1 Document (1.16 seconds)

BMRB: 15747

2K3C

Structural and Functional Characterization of TM IX of the NHE1 Isoform of the Na+/H+ Exchanger

Authors

Reddy, T., Ding, J., Li, X., Sykes, B.D., Fliegel, L., Rainey, J.K.

Assembly

TMIX peptide

Entity

1. TMIX peptide (polymer, Thiol state: not present), 33 monomers, 3437.170 Da Detail

XKSYMAYLSA ELFHLSGIMA LIASGVVMRP KKX

Formula weight

3437.17 Da

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 93.9 %, Completeness: 83.4 %, Completeness (bb): 73.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C
All	83.4 % (282 of 338)	97.4 % (185 of 190)	65.5 % (97 of 148)
Backbone	73.4 % (113 of 154)	100.0 % (63 of 63)	54.9 % (50 of 91)
Sidechain	91.1 % (194 of 213)	96.1 % (122 of 127)	83.7 % (72 of 86)
Aromatic	93.3 % (28 of 30)	93.3 % (14 of 15)	93.3 % (14 of 15)
Methyl	95.0 % (38 of 40)	100.0 % (20 of 20)	90.0 % (18 of 20)

1. TMIX peptide

XKSYMAYLSA ELFHLSGIMA LIASGVVMRP KKX

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303.15 K, pH 5.05, Details 0.9 0.1 mM synthetic peptide in a 95% H2O, 5% D2O solution containing ~75 mM DPC-d38 and 0.25 mM (d6)-2,2-dimethyl-2-silapentane-5-sulfonic acid (DSS) for chemical shift referencing. Solution pH was adjusted to 5.05.

#	Name	Isotope labeling	Concentration
1	TMIX peptide	natural abundance	0.9 (±0.1) mM
2	DPC-d38		75 mM
3	DSS		0.25 mM
4	H2O		95 %
5	D2O		5 %

Protein Blocks Logo

Calculated from 40 models in PDB: 2K3C, Strand ID: A Detail

Release date

2008-05-28

Citation

Structural and functional characterization of transmembrane segment IX of the NHE1 isoform of the Na+/H+ exchanger
Li, X., Reddy, T., Ding, J., Sykes, B.D., Rainey, J.K., Fliegel, L.
J. Biol. Chem. (2008), 283, 22018-22030, PubMed 18508767 , DOI 10.1074/jbc.M803447200 , Abstract

Related entities 1. TMIX peptide, : 1 : 10 : 11 entities Detail

Interaction partners 1. TMIX peptide, : 13 interactors Detail

More details for 13 interactors identified by 6 citations

Experiments performed 3 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15747_2k3c.nef
Input source #2: Coordindates	2k3c.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	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:2:LYS:N	1:1:ACE:C	unknown	unknown	n/a
1:32:LYS:C	1:33:NH2:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	336	ACE	ACETYL GROUP	Assigned chemical shifts, Coordinates
A	368	NH2	AMINO GROUP	Coordinates

Sequence alignments

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

--340-------350-------360--------
XKSYMAYLSAELFHLSGIMALIASGVVMRPKKX
|||||||||||||||||||||||||||||||||
XKSYMAYLSAELFHLSGIMALIASGVVMRPKKX
--------10--------20--------30---

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	33	0	0	100.0

Content subtype: combined_15747_2k3c.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	298		87.9 (chain: A, length: 33)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	2472 (1)	noe	93.9 (chain: A, length: 33)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	171 (1)	noe	42.4 (chain: A, length: 33)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	27 (27)	.	63.6 (chain: A, length: 33)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 33, Sequence coverage: 87.9%
- Total number of assignments
  - ¹H chemical shifts: 205
  - ¹³C chemical shifts: 93
- Completeness of assignments
- Peptide bond of PRO
- 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: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 33, Sequence coverage: 93.9%
- Total number of restraints: 2321
- Weight of restraints: 1.0 (2321)
- Potential type of restraints: square-well-parabolic (2321)
- Range of distance target values: 2.3, 3.9 (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
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: OK
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 33, Sequence coverage: 42.4%
  - Total number of restraints: 171
  - Weight of restraints: 1.0 (171)
  - Potential type of restraints: square-well-parabolic (171)
  - Range of distance target values: 2.3, 3.9 (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_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 33, Sequence coverage: 63.6%
- Total number of restraints: 27
- Total number of restraints per polymer type: 27
- Weight of restraints: 1.0 (27)
- Potential type of restraints: square-well-parabolic (27)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords membrane peptide, dodecylphosphocholine micelle, NHE1, Na+/H+ transporter

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Found 1 Document (1.16 seconds)

BMRB: 15747

Sample

Related entities 1. TMIX peptide, : 1 : 10 : 11 entities Detail

Interaction partners 1. TMIX peptide, : 13 interactors Detail

Experiments performed 3 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail