BMRBj - BMREntryMaster

Found 1 Document (0.804 seconds)

BMRB: 30604

6OQH

Solution NMR structure of a quiet outer membrane protein G Nanopore (OmpG mutant: Delta-L6-D215)

Authors

Sanganna Gari, R.R., Seelheim, P., Liang, B., Tamm, L.K.

Assembly

Outer membrane protein G

Entity

1. Outer membrane protein G (polymer, Thiol state: not present), 271 monomers, 31473.78 Da Detail

EERNDWHFNI GAMYEIENVE GYGEDMDGLA EPSVYFNAAN GPWRIALAYY QEGPVDYSAG KRGTWFDRPE LEVHYQFLEN DDFSFGLTGG FRNYGYHYVD EPGKDTANMQ RWKIAPDWDV KLTDDLRFNG WLSMYKFAND LNTTGYADTR VETETGLQYT FNETVALRVN YYLERGFNMD DSRNNGEFST QEIRAYLPLT LGNHSVTPYT RIGLRWSNGE GHDFNRVGLF YGYDFQNGLS VSLEYAFEWQ DHDEGDSDKF HYAGVGVNYS F

Formula weight

31473.78 Da

Source organism

Escherichia coli K-12

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 95.6 %, Completeness: 42.1 %, Completeness (bb): 76.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	42.1 % (1334 of 3171)	21.4 % (350 of 1634)	59.9 % (742 of 1238)	80.9 % (242 of 299)
Backbone	76.4 % (1230 of 1610)	48.6 % (273 of 562)	92.0 % (722 of 785)	89.4 % (235 of 263)
Sidechain	17.6 % (317 of 1804)	6.8 % (73 of 1072)	34.2 % (238 of 696)	16.7 % (6 of 36)
Aromatic	1.7 % (8 of 480)	1.7 % (4 of 240)	0.0 % (0 of 232)	50.0 % (4 of 8)
Methyl	19.0 % (41 of 216)	14.8 % (16 of 108)	23.1 % (25 of 108)

1. entity 1

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 6.3, Details 1 mM [U-13C; U-15N; U-2H] OmpG delta-L6-D215 mutant, 200 mM DPC, 25 mM Bis-Tris, 50 mM sodium chloride, 0.05 % w/v sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	OmpG delta-L6-D215 mutant	[U-13C; U-15N; U-2H]	1 mM
2	DPC	natural abundance	200 mM
3	Bis-Tris	natural abundance	25 mM
4	sodium chloride	natural abundance	50 mM
5	sodium azide	natural abundance	0.05 % w/v

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	indirect	0.2514495
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.1013291

Referencing offset: 0.31 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	indirect	0.2514495
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.1013291

Referencing offset: 0.31 ppm, Outliers: 2 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	indirect	0.2514495
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.1013291

Referencing offset: 0.8 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 6OQH, Strand ID: A Detail

Release date

2019-05-27

Citation

Quiet Outer Membrane Protein G (OmpG) Nanopore for Biosensing
Sanganna Gari, R.R., Seelheim, P., Liang, B., Tamm, L.K.
ACS. Sens. (2019), 4, 1230-1235, PubMed 30990011 , DOI 10.1021/acssensors.8b01645 , Abstract

Related entities 1. Outer membrane protein G, : 1 : 11 entities Detail

Interaction partners 1. Outer membrane protein G, : 3 interactors Detail

More details for 3 interactors identified by 1 citations

Experiments performed 7 experiments Detail

1 3D HNCA

Instrument

Bruker AVANCE III - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 6.3, Details 1 mM [U-13C; U-15N; U-2H] OmpG delta-L6-D215 mutant, 200 mM DPC, 25 mM Bis-Tris, 50 mM sodium chloride, 0.05 % w/v sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	OmpG delta-L6-D215 mutant	[U-13C; U-15N; U-2H]	1 mM
2	DPC	natural abundance	200 mM
3	Bis-Tris	natural abundance	25 mM
4	sodium chloride	natural abundance	50 mM
5	sodium azide	natural abundance	0.05 % w/v

2 3D HNCACB

Instrument

Bruker AVANCE III - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	OmpG delta-L6-D215 mutant	[U-13C; U-15N; U-2H]	1 mM
2	DPC	natural abundance	200 mM
3	Bis-Tris	natural abundance	25 mM
4	sodium chloride	natural abundance	50 mM
5	sodium azide	natural abundance	0.05 % w/v

3 3D HNCO

Instrument

Bruker AVANCE III - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	OmpG delta-L6-D215 mutant	[U-13C; U-15N; U-2H]	1 mM
2	DPC	natural abundance	200 mM
3	Bis-Tris	natural abundance	25 mM
4	sodium chloride	natural abundance	50 mM
5	sodium azide	natural abundance	0.05 % w/v

4 3D HN(CA)CO

Instrument

Bruker AVANCE III - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	OmpG delta-L6-D215 mutant	[U-13C; U-15N; U-2H]	1 mM
2	DPC	natural abundance	200 mM
3	Bis-Tris	natural abundance	25 mM
4	sodium chloride	natural abundance	50 mM
5	sodium azide	natural abundance	0.05 % w/v

5 3D 15N-1H-1H NOESY-TROSY

Instrument

Bruker AVANCE III - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	OmpG delta-L6-D215 mutant	[U-13C; U-15N; U-2H]	1 mM
2	DPC	natural abundance	200 mM
3	Bis-Tris	natural abundance	25 mM
4	sodium chloride	natural abundance	50 mM
5	sodium azide	natural abundance	0.05 % w/v

6 3D 15N-1H-15N HSQC-NOESY-HSQC

Instrument

Bruker AVANCE III - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	OmpG delta-L6-D215 mutant	[U-13C; U-15N; U-2H]	1 mM
2	DPC	natural abundance	200 mM
3	Bis-Tris	natural abundance	25 mM
4	sodium chloride	natural abundance	50 mM
5	sodium azide	natural abundance	0.05 % w/v

7 2D 1H-15N HSQC

Instrument

Bruker AVANCE III - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	OmpG delta-L6-D215 mutant	[U-13C; U-15N; U-2H]	1 mM
2	DPC	natural abundance	200 mM
3	Bis-Tris	natural abundance	25 mM
4	sodium chloride	natural abundance	50 mM
5	sodium azide	natural abundance	0.05 % w/v

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr30604_3.str
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

None

Content subtype: bmr30604_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1199		95.2 (chain: 1, length: 271)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 271, Sequence coverage: 95.2%
- Total number of assignments
  - ¹³C chemical shifts: 725
  - ¹H chemical shifts: 237
  - ¹⁵N chemical shifts: 237
- Completeness of assignments
  - Entity_assemble_ID: 1
- Peptide bond of PRO
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	1238	725	58.6
¹H chemical shifts	1634	237	14.5
¹⁵N chemical shifts	314	237	75.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	542	506	93.4
¹H chemical shifts	562	233	41.5
¹⁵N chemical shifts	263	233	88.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	696	219	31.5
¹H chemical shifts	1072	4	0.4
¹⁵N chemical shifts	51	4	7.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	113	13	11.5
¹H chemical shifts	113	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	232	0	0.0
¹H chemical shifts	240	4	1.7
¹⁵N chemical shifts	8	4	50.0

Keywords MEMBRANE PROTEIN, Outer membrane protein b-barrel Solution NMR

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Found 1 Document (0.804 seconds)

BMRB: 30604

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Outer membrane protein G, : 1 : 11 entities Detail

Interaction partners 1. Outer membrane protein G, : 3 interactors Detail

Experiments performed 7 experiments Detail

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Chemical shift validation 3 contents Detail