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BMRB: 16678

2KSY

1H, 13C and 15N Chemical Shift Assignments for Sensory Rhodopsin II

Authors

Gautier, A., Mott, H.R., Bostock, M.J., Kirkpatrick, J.P., Nietlispach, D.

Assembly

Sensory Rhodopsin II

Entity

1. Sensory Rhodopsin II (polymer, Thiol state: not present), 247 monomers, 26704.18 Da Detail

MVGLTTLFWL GAIGMLVGTL AFAWAGRDAG SGERRYYVTL VGISGIAAVA YAVMALGVGW VPVAERTVFV PRYIDWILTT PLIVYFLGLL AGLDSREFGI VITLNTVVML AGFAGAMVPG IERYALFGMG AVAFIGLVYY LVGPMTESAS QRSSGIKSLY VRLRNLTVVL WAIYPFIWLL GPPGVALLTP TVDVALIVYL DLVTXVGFGF IALDAAATLR AEHGESLAGV DTDTPAVADL EHHHHHH

Formula weight

26704.18 Da

Source organism

Natronomonas pharaonis

Exptl. method

Refine. method

DGSA-distance geometry simulated annealing, molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.6 %, Completeness: 87.3 %, Completeness (bb): 94.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	87.3 % (2419 of 2772)	83.7 % (1159 of 1385)	89.5 % (1022 of 1142)	97.1 % (238 of 245)
Backbone	94.5 % (1376 of 1456)	92.2 % (470 of 510)	95.4 % (677 of 710)	97.0 % (229 of 236)
Sidechain	80.8 % (1240 of 1534)	78.1 % (683 of 875)	84.3 % (548 of 650)	100.0 % (9 of 9)
Aromatic	82.6 % (246 of 298)	85.2 % (127 of 149)	79.0 % (113 of 143)	100.0 % (6 of 6)
Methyl	98.5 % (400 of 406)	98.5 % (200 of 203)	98.5 % (200 of 203)

1. Sensory Rhodopsin II

MVGLTTLFWL GAIGMLVGTL AFAWAGRDAG SGERRYYVTL VGISGIAAVA YAVMALGVGW VPVAERTVFV PRYIDWILTT PLIVYFLGLL AGLDSREFGI VITLNTVVML AGFAGAMVPG IERYALFGMG AVAFIGLVYY LVGPMTESAS QRSSGIKSLY VRLRNLTVVL WAIYPFIWLL GPPGVALLTP TVDVALIVYL DLVTXVGFGF IALDAAATLR AEHGESLAGV DTDTPAVADL EHHHHHH

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 323 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	SENSORY RHODOPSIN II	[U-100% 15N]		0.5 mM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		50 mM
4	sodium azide	natural abundance		0.05 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 323 K, pH 6

#	Name	Isotope labeling	Type	Concentration
5	SENSORY RHODOPSIN II	[U-100% 13C; U-100% 15N]		0.5 mM
6	sodium chloride	natural abundance		50 mM
7	sodium phosphate	natural abundance		50 mM
8	sodium azide	natural abundance		0.05 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 323 K, pH 6

#	Name	Isotope labeling	Type	Concentration
9	SENSORY RHODOPSIN II	[U-13C; U-15N; U-2H]		0.5 mM
10	sodium chloride	natural abundance		50 mM
11	sodium phosphate	natural abundance		50 mM
12	sodium azide	natural abundance		0.05 %

Protein Blocks Logo

Calculated from 30 models in PDB: 2KSY, Strand ID: A Detail

Release date

2010-05-31

Citation

Structure determination of the seven-helix transmembrane receptor sensory rhodopsin II by solution NMR spectroscopy
Gautier, A., Mott, H.R., Bostock, M.J., Kirkpatrick, J.P., Nietlispach, D.
Nat. Struct. Mol. Biol. (2010), 17, 768-774, PubMed 20512150 , DOI 10.1038/nsmb.1807 , Abstract

Related entities 1. Sensory Rhodopsin II, : 1 : 1 : 119 entities Detail

Interaction partners 1. Sensory Rhodopsin II, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 323 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	SENSORY RHODOPSIN II	[U-100% 15N]		0.5 mM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		50 mM
4	sodium azide	natural abundance		0.05 %

2 2D 1H-13C HSQC

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 323 K, pH 6

#	Name	Isotope labeling	Type	Concentration
5	SENSORY RHODOPSIN II	[U-100% 13C; U-100% 15N]		0.5 mM
6	sodium chloride	natural abundance		50 mM
7	sodium phosphate	natural abundance		50 mM
8	sodium azide	natural abundance		0.05 %

3 3D HNCA

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 323 K, pH 6

#	Name	Isotope labeling	Type	Concentration
9	SENSORY RHODOPSIN II	[U-13C; U-15N; U-2H]		0.5 mM
10	sodium chloride	natural abundance		50 mM
11	sodium phosphate	natural abundance		50 mM
12	sodium azide	natural abundance		0.05 %

4 3D HN(CO)CA

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 323 K, pH 6

#	Name	Isotope labeling	Type	Concentration
9	SENSORY RHODOPSIN II	[U-13C; U-15N; U-2H]		0.5 mM
10	sodium chloride	natural abundance		50 mM
11	sodium phosphate	natural abundance		50 mM
12	sodium azide	natural abundance		0.05 %

5 3D HNCO

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 323 K, pH 6

#	Name	Isotope labeling	Type	Concentration
9	SENSORY RHODOPSIN II	[U-13C; U-15N; U-2H]		0.5 mM
10	sodium chloride	natural abundance		50 mM
11	sodium phosphate	natural abundance		50 mM
12	sodium azide	natural abundance		0.05 %

6 3D HN(CA)CO

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 323 K, pH 6

#	Name	Isotope labeling	Type	Concentration
9	SENSORY RHODOPSIN II	[U-13C; U-15N; U-2H]		0.5 mM
10	sodium chloride	natural abundance		50 mM
11	sodium phosphate	natural abundance		50 mM
12	sodium azide	natural abundance		0.05 %

7 3D HN(CA)CB

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 323 K, pH 6

#	Name	Isotope labeling	Type	Concentration
9	SENSORY RHODOPSIN II	[U-13C; U-15N; U-2H]		0.5 mM
10	sodium chloride	natural abundance		50 mM
11	sodium phosphate	natural abundance		50 mM
12	sodium azide	natural abundance		0.05 %

8 3D HN(COCA)CB

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 323 K, pH 6

#	Name	Isotope labeling	Type	Concentration
9	SENSORY RHODOPSIN II	[U-13C; U-15N; U-2H]		0.5 mM
10	sodium chloride	natural abundance		50 mM
11	sodium phosphate	natural abundance		50 mM
12	sodium azide	natural abundance		0.05 %

9 3D 1H-15N NOESY

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 323 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	SENSORY RHODOPSIN II	[U-100% 15N]		0.5 mM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		50 mM
4	sodium azide	natural abundance		0.05 %

10 3D 1H-13C NOESY

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 323 K, pH 6

#	Name	Isotope labeling	Type	Concentration
5	SENSORY RHODOPSIN II	[U-100% 13C; U-100% 15N]		0.5 mM
6	sodium chloride	natural abundance		50 mM
7	sodium phosphate	natural abundance		50 mM
8	sodium azide	natural abundance		0.05 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_16678_2ksy.nef
Input source #2: Coordindates	2ksy.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)
1:205:LYS:NZ	2:1:RET:C15	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	RET	RETINAL	None

Sequence alignments

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

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

-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200
VITLNTVVMLAGFAGAMVPGIERYALFGMGAVAFIGLVYYLVGPMTESASQRSSGIKSLYVRLRNLTVVLWAIYPFIWLLGPPGVALLTPTVDVALIVYL
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
VITLNTVVMLAGFAGAMVPGIERYALFGMGAVAFIGLVYYLVGPMTESASQRSSGIKSLYVRLRNLTVVLWAIYPFIWLLGPPGVALLTPTVDVALIVYL

-------210-------220-------230-------240-------
DLVTKVGFGFIALDAAATLRAEHGESLAGVDTDTPAVADLEHHHHHH
|||||||||||||||||||||||||||||||||||||||||||||||
DLVTKVGFGFIALDAAATLRAEHGESLAGVDTDTPAVADLEHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	247	0	0	100.0

Content subtype: combined_16678_2ksy.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	1		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	2359		96.8 (chain: A, length: 247)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	16257 (1)	noe	93.9 (chain: A, length: 247)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 247, Sequence coverage: 96.8%
- Total number of assignments
  - ¹H chemical shifts: 1116
  - ¹³C chemical shifts: 1004
  - ¹⁵N chemical shifts: 239
- Completeness of assignments
- 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: CNS/XPLOR_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 247, Sequence coverage: 93.9%
- Total number of restraints: 16207
- Weight of restraints: 1.0 (16207)
- Potential type of restraints: square-well-parabolic (16207)
- Range of distance target values: 1.7, 6.75 (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

Keywords membrane proteins, NMR spectroscopy, protein structures, receptors, structure elucidation