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BMRB: 19892

2MNH

REFINED STRUCTURE OF OUTER MEMBRANE PROTEIN X IN NANODISC BY MEASURING RESIDUAL DIPOLAR COUPLINGS

Authors

Bibow, S., Carneiro, M.G., Sabo, T.M., Schwiegk, C., Becker, S., Riek, R., Lee, D.

Assembly

OUTER MEMBRANE PROTEIN X IN NANODISC

Entity

1. OUTER MEMBRANE PROTEIN X IN NANODISC (polymer, Thiol state: not present), 148 monomers, 16359.65 Da Detail

ATSTVTGGYA QSDAQGQMNK MGGFNLKYRY EEDNSPLGVI GSFTYTEKSR TASSGDYNKN QYYGITAGPA YRINDWASIY GVVGVGYGKF QTTEYPTYKN DTSDYGFSYG AGLQFNPMEN VALDFSYEQS RIRSVDVGTW IAGVGYRF

Formula weight

16359.65 Da

Source organism

Escherichia coli

Exptl. method

NMR

Refine. method

SIMULATED ANNEALING

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 79.7 %, Completeness: 23.5 %, Completeness (bb): 51.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹⁵N
All	23.5 % (239 of 1019)	14.2 % (122 of 857)	72.2 % (117 of 162)
Backbone	51.5 % (235 of 456)	37.8 % (118 of 312)	81.3 % (117 of 144)
Sidechain	0.7 % (4 of 563)	0.7 % (4 of 545)	0.0 % (0 of 18)
Aromatic	3.5 % (4 of 113)	3.6 % (4 of 111)	0.0 % (0 of 2)
Methyl	0.0 % (0 of 60)	0.0 % (0 of 60)

1. OUTER MEMBRANE PROTEIN X

ATSTVTGGYA QSDAQGQMNK MGGFNLKYRY EEDNSPLGVI GSFTYTEKSR TASSGDYNKN QYYGITAGPA YRINDWASIY GVVGVGYGKF QTTEYPTYKN DTSDYGFSYG AGLQFNPMEN VALDFSYEQS RIRSVDVGTW IAGVGYRF

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 7.4, Details 10 MM TRIS-HCL, 100 MM NACL, 1 MM EDTA, 0.05 % SODIUM AZIDE, 0.5 MM

#	Name	Isotope labeling	Concentration
1	OUTER MEMBRANE PROTEIN X	[U-100% 13C; U-100% 15N]	0.5 mM
2	Tris-HCl	natural abundance	10 mM
3	sodium azide	natural abundance	0.05 %
4	NaCl	natural abundance	100 mM
5	EDTA	natural abundance	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

Protein Blocks Logo

Calculated from 10 models in PDB: 2MNH, Strand ID: A Detail

Release date

2014-04-13

Citation

Measuring membrane protein bond orientations in nanodiscs via residual dipolar couplings
Bibow, S., Carneiro, M.G., Sabo, T.M., Schwiegk, C., Becker, S., Riek, R., Lee, D.
Protein Sci. (2014), 23, 851-856, PubMed 24752984 , DOI 10.1002/pro.2482 , Abstract

Related entities 1. OUTER MEMBRANE PROTEIN X IN NANODISC, : 1 : 5 : 4 : 10 entities Detail

Experiments performed 4 experiments Detail

1 3D 1H-15N NOESY

Instrument

Bruker AVANCE I and AVANCE III - na MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 7.4, Details 10 MM TRIS-HCL, 100 MM NACL, 1 MM EDTA, 0.05 % SODIUM AZIDE, 0.5 MM

#	Name	Isotope labeling	Concentration
1	OUTER MEMBRANE PROTEIN X	[U-100% 13C; U-100% 15N]	0.5 mM
2	Tris-HCl	natural abundance	10 mM
3	sodium azide	natural abundance	0.05 %
4	NaCl	natural abundance	100 mM
5	EDTA	natural abundance	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

2 3D HNCA

Instrument

Bruker AVANCE I and AVANCE III - na MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 7.4, Details 10 MM TRIS-HCL, 100 MM NACL, 1 MM EDTA, 0.05 % SODIUM AZIDE, 0.5 MM

#	Name	Isotope labeling	Concentration
1	OUTER MEMBRANE PROTEIN X	[U-100% 13C; U-100% 15N]	0.5 mM
2	Tris-HCl	natural abundance	10 mM
3	sodium azide	natural abundance	0.05 %
4	NaCl	natural abundance	100 mM
5	EDTA	natural abundance	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

3 2D 1H-15N HSQC

Instrument

Bruker AVANCE I and AVANCE III - na MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 7.4, Details 10 MM TRIS-HCL, 100 MM NACL, 1 MM EDTA, 0.05 % SODIUM AZIDE, 0.5 MM

#	Name	Isotope labeling	Concentration
1	OUTER MEMBRANE PROTEIN X	[U-100% 13C; U-100% 15N]	0.5 mM
2	Tris-HCl	natural abundance	10 mM
3	sodium azide	natural abundance	0.05 %
4	NaCl	natural abundance	100 mM
5	EDTA	natural abundance	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

4 2D 1H-15N COCAINE

Instrument

Bruker AVANCE I and AVANCE III - na MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 318 K, pH 7.4, Details 10 MM TRIS-HCL, 100 MM NACL, 1 MM EDTA, 0.05 % SODIUM AZIDE, 0.5 MM

#	Name	Isotope labeling	Concentration
1	OUTER MEMBRANE PROTEIN X	[U-100% 13C; U-100% 15N]	0.5 mM
2	Tris-HCl	natural abundance	10 mM
3	sodium azide	natural abundance	0.05 %
4	NaCl	natural abundance	100 mM
5	EDTA	natural abundance	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

NMR combined restraints 7 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_19892_2mnh.nef
Input source #2: Coordindates	2mnh.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	Error

Disulfide bonds

None

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--------60--------70--------80--------90-------100
ATSTVTGGYAQSDAQGQMNKMGGFNLKYRYEEDNSPLGVIGSFTYTEKSRTASSGDYNKNQYYGITAGPAYRINDWASIYGVVGVGYGKFQTTEYPTYKN
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ATSTVTGGYAQSDAQGQMNKMGGFNLKYRYEEDNSPLGVIGSFTYTEKSRTASSGDYNKNQYYGITAGPAYRINDWASIYGVVGVGYGKFQTTEYPTYKN

-------110-------120-------130-------140--------
DTSDYGFSYGAGLQFNPMENVALDFSYEQSRIRSVDVGTWIAGVGYRF
||||||||||||||||||||||||||||||||||||||||||||||||
DTSDYGFSYGAGLQFNPMENVALDFSYEQSRIRSVDVGTWIAGVGYRF

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	148	0	0	100.0

Content subtype: combined_19892_2mnh.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	OK	235		79.7 (chain: A, length: 148)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	58 (1)	noe	66.2 (chain: A, length: 148)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	Error	170 (1)	hbond	58.1 (chain: A, length: 148)
3	Distance restraints	CNS/XPLOR_distance_constraints_5	Error	170 (1)	hbond	58.1 (chain: A, length: 148)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	194 (194)	.	86.5 (chain: A, length: 148)
1	RDC restraints	DYANA/DIANA_dipolar_coupling_6	OK	87 (87)	.	58.8 (chain: A, length: 148)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 148, Sequence coverage: 79.7%
- Total number of assignments
  - ¹H chemical shifts: 118
  - ¹⁵N chemical shifts: 117
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	857	118	13.8
¹⁵N chemical shifts	168	117	69.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	312	118	37.8
¹⁵N chemical shifts	144	117	81.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	545	0	0.0
¹⁵N chemical shifts	24	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	63	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	111	0	0.0
¹⁵N chemical shifts	2	0	0.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 148, Sequence coverage: 66.2%
- Total number of restraints: 58
- Weight of restraints: 1.0 (58)
- Potential type of restraints: square-well-parabolic (58)
- Range of distance target values: 1.15, 2.5 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_4
  - Status: Error
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 148, Sequence coverage: 58.1%
  - Total number of restraints: 170
  - Weight of restraints: 1.0 (170)
  - Potential type of restraints: square-well-parabolic (170)
  - Range of distance target values: 1.3, 1.75 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_5
    - Status: Error
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 148, Sequence coverage: 58.1%
    - Total number of restraints: 170
    - Weight of restraints: 1.0 (170)
    - Potential type of restraints: lower-bound-parabolic (170)
    - Range of distance target values: 1.8, 2.6 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
    - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 148, Sequence coverage: 86.5%
- Total number of restraints: 194
- Total number of restraints per polymer type: 194
- Weight of restraints: 1.0 (194)
- Potential type of restraints: square-well-parabolic (194)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: DYANA/DIANA_dipolar_coupling_6

Status: OK
Experiment type: .

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 148, Sequence coverage: 58.8%

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
ATSTVTGGYAQSDAQGQMNKMGGFNLKYRYEEDNSPLGVIGSFTYTEKSRTASSGDYNKNQYYGITAGPAYRINDWASIYGVVGVGYGKFQTTEYPTYKN
 | |||||     | || ||||| |||| |||| | ||||| ||| |       || |||| |||||| |||       || ||||    |   |   | 
.T.TVTGG.....A.GQ.NKMGG.NLKY.YEED.S.LGVIG.FTY.E.......GD.NKNQ.YGITAG.AYR.......YG.VGVG....Q...Y...K.

-------110-------120-------130-------140--------
DTSDYGFSYGAGLQFNPMENVALDFSYEQSRIRSVDVGTWIAGVGYRF
 |||||| || ||| | | ||||||      || ||||    ||||||
.TSDYGF.YG.GLQ.N.M.NVALDF......IR.VDVG....GVGYRF

Total number of restraints: 87
Potential type of restraints: undefined (87)
Range of observed RDC values: 100.0, -100.0 (Hz)
RDC restraints per residue
- Chain_ID: A
  None

Keywords BETA BARREL, MEMBRANE PROTEIN, NANODISC, OMPX, RESIDUAL DIPOLAR COUPLING

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Found 1 Document (0.724 seconds)

BMRB: 19892

Sample

Related entities 1. OUTER MEMBRANE PROTEIN X IN NANODISC, : 1 : 5 : 4 : 10 entities Detail

Experiments performed 4 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 7 contents Detail