BMRBj - BMREntryMaster

Found 1 Document (0.886 seconds)

BMRB: 15651

2K0L

NMR structure of the transmembrane domain of the Outer Membrane Protein A from Klebsiella pneumoniae in DHPC micelles.

Authors

Renault, M., Saurel, O., Gervais, V., Lohr, F., Reat, V., Piotto, M., Milon, A.

Assembly

KpOmpA transmembrane domain

Entity

1. KpOmpA transmembrane domain (polymer, Thiol state: not present), 216 monomers, 23369.57 Da Detail

ARIMKAIFVL NAAPKDNTWY AGGKLGWSQY HDTGFYGNGF QNNNGPTRND QLGAGAFGGY QVNPYLGFEM GYDWLGRMAY KGSVDNGAFK AQGVQLTAKL GYPITDDLDI YTRLGGMVWR ADSKGNYAST GVSRSEHDTG VSPVFAGGVE WAVTRDIATR LEYQWVNNIG DAGTVGTRPD NGMLSLGVSY RFGQEDAAPV VAPAPAPAPE HHHHHH

Formula weight

23369.57 Da

Source organism

Klebsiella pneumoniae

Exptl. method

solution NMR

Refine. method

DGSA-distance geometry simulated annealing, simulated annealing, torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 88.4 %, Completeness: 53.2 %, Completeness (bb): 74.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	53.2 % (1275 of 2395)	32.7 % (402 of 1229)	74.3 % (694 of 934)	77.2 % (179 of 232)
Backbone	74.2 % (945 of 1274)	50.7 % (229 of 452)	87.7 % (541 of 617)	85.4 % (175 of 205)
Sidechain	37.7 % (493 of 1306)	22.3 % (173 of 777)	62.7 % (315 of 502)	18.5 % (5 of 27)
Aromatic	2.9 % (8 of 280)	4.3 % (6 of 140)	0.0 % (0 of 134)	33.3 % (2 of 6)
Methyl	80.7 % (163 of 202)	68.3 % (69 of 101)	93.1 % (94 of 101)

1. KpOmpA transmembrane domain

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 6.5, Details 1mM protein, 300 mM DHPC, 20 mM NaH2PO4, 100 mM NaCl.

#	Name	Isotope labeling	Concentration
1	KpOmpA transmembrane domain	[U-13C; U-15N; U-2H]	1 mM
2	DHPC		300 mM
3	NaH2PO4		20 mM
4	NaCl		100 mM
5	H2O	natural abundance	90 %
6	D2O		10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 6.5, Details 1mM protein, 300 mM DHPC, 20 mM NaH2PO4, 100 mM NaCl.

#	Name	Isotope labeling	Concentration
7	KpOmpA transmembrane domain	[U-13C; U-15N; U-2H]/[L,V,I(delta1)-13CH3]	1 mM
8	DHPC		300 mM
9	NaH2PO4		20 mM
10	NaCl		100 mM
11	H2O	natural abundance	90 %
12	D2O		10 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 6.5, Details 1mM protein, 300 mM DHPC(d22), 20 mM NaH2PO4, 100 mM NaCl.

#	Name	Isotope labeling	Concentration
13	KpOmpA transmembrane domain	[U-15N; 10% 13C]	1 mM
14	DHPC		300 mM
15	NaH2PO4		20 mM
16	NaCl		100 mM
17	H2O	natural abundance	90 %
18	D2O		10 %

Sample #4

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 6.5, Details 1mM protein, 300 mM DHPC(d22), 20 mM NaH2PO4, 100 mM NaCl.

#	Name	Isotope labeling	Concentration
19	KpOmpA transmembrane domain	[U-13C; U-15N; U-2H]/[L,V,I(delta1)-13CH3]	1 mM
20	DHPC		300 mM
21	NaH2PO4		20 mM
22	NaCl		100 mM
23	H2O	natural abundance	90 %
24	D2O		10 %

LACS Plot; CA

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

Referencing offset: 0.54 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: 0.54 ppm, Outliers: 1 Detail

LACS Plot; CO

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

Referencing offset: 0.65 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2K0L, Strand ID: A Detail

Release date

2008-11-03

Citation

Solution state NMR structure and dynamics of KpOmpA, a 210 residue transmembrane domain possessing a high potential for immunological applications
Renault, M., Saurel, O., Czaplicki, J., Demange, P., Gervais, V., Lohr, F., Reat, V., Piotto, M., Milon, A.
J. Mol. Biol. (2009), 385, 117-130, PubMed 18952100 , DOI 10.1016/j.jmb.2008.10.021 , Abstract

Related entities 1. KpOmpA transmembrane domain, : 1 : 1 : 24 entities Detail

Experiments performed 12 experiments Detail

1 2D [15N,1H]-TROSY

Instrument

Bruker Avance - 900 MHz Four radio-frequency 1H, 2H, 13C, 15N channels, 1H-{13C, 15N}-triple resonance cryoprobe, z-gradient coil.

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 6.5, Details 1mM protein, 300 mM DHPC, 20 mM NaH2PO4, 100 mM NaCl.

#	Name	Isotope labeling	Concentration
1	KpOmpA transmembrane domain	[U-13C; U-15N; U-2H]	1 mM
2	DHPC		300 mM
3	NaH2PO4		20 mM
4	NaCl		100 mM
5	H2O	natural abundance	90 %
6	D2O		10 %

2 3D [15N,1H]-TROSY-HNCACB

Instrument

Bruker Avance - 900 MHz Four radio-frequency 1H, 2H, 13C, 15N channels, 1H-{13C, 15N}-triple resonance cryoprobe, z-gradient coil.

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 6.5, Details 1mM protein, 300 mM DHPC, 20 mM NaH2PO4, 100 mM NaCl.

#	Name	Isotope labeling	Concentration
1	KpOmpA transmembrane domain	[U-13C; U-15N; U-2H]	1 mM
2	DHPC		300 mM
3	NaH2PO4		20 mM
4	NaCl		100 mM
5	H2O	natural abundance	90 %
6	D2O		10 %

3 3D [15N,1H]-TROSY-HN(CO)CACB

Instrument

Bruker Avance - 600 MHz Four radio-frequency 1H, 2H, 13C, 15N channels, 1H-{13C, 15N}-triple resonance cryoprobe, z-gradient coil.

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 6.5, Details 1mM protein, 300 mM DHPC, 20 mM NaH2PO4, 100 mM NaCl.

#	Name	Isotope labeling	Concentration
1	KpOmpA transmembrane domain	[U-13C; U-15N; U-2H]	1 mM
2	DHPC		300 mM
3	NaH2PO4		20 mM
4	NaCl		100 mM
5	H2O	natural abundance	90 %
6	D2O		10 %

4 3D [15N,1H]-TROSY-HNCO

Instrument

Bruker Avance - 700 MHz Three radio-frequency 1H, 13C, 15N channels, 1H-{13C, 15N}-triple resonance probe, z-gradient coil.

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 6.5, Details 1mM protein, 300 mM DHPC, 20 mM NaH2PO4, 100 mM NaCl.

#	Name	Isotope labeling	Concentration
1	KpOmpA transmembrane domain	[U-13C; U-15N; U-2H]	1 mM
2	DHPC		300 mM
3	NaH2PO4		20 mM
4	NaCl		100 mM
5	H2O	natural abundance	90 %
6	D2O		10 %

5 3D [15N,1H]-TROSY-HN(CA)CO

Instrument

Bruker Avance - 600 MHz Four radio-frequency 1H, 2H, 13C, 15N channels, 1H-{13C, 15N}-triple resonance cryoprobe, z-gradient coil.

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 6.5, Details 1mM protein, 300 mM DHPC, 20 mM NaH2PO4, 100 mM NaCl.

#	Name	Isotope labeling	Concentration
1	KpOmpA transmembrane domain	[U-13C; U-15N; U-2H]	1 mM
2	DHPC		300 mM
3	NaH2PO4		20 mM
4	NaCl		100 mM
5	H2O	natural abundance	90 %
6	D2O		10 %

6 3D (HNCA)CC-TOCSY-(CA)-[15N,1H]-TROSY

Instrument

Bruker Avance - 800 MHz Four radio-frequency 1H, 2H, 13C, 15N channels, 1H-{13C, 15N}-triple resonance cryoprobe, z-gradient coil.

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 6.5, Details 1mM protein, 300 mM DHPC, 20 mM NaH2PO4, 100 mM NaCl.

#	Name	Isotope labeling	Concentration
1	KpOmpA transmembrane domain	[U-13C; U-15N; U-2H]	1 mM
2	DHPC		300 mM
3	NaH2PO4		20 mM
4	NaCl		100 mM
5	H2O	natural abundance	90 %
6	D2O		10 %

7 3D (H)C(CC)-TOCSY-(CA)-[15N,1H]-TROSY

Instrument

Bruker Avance - 800 MHz Four radio-frequency 1H, 2H, 13C, 15N channels, 1H-{13C, 15N}-triple resonance cryoprobe, z-gradient coil.

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 6.5, Details 1mM protein, 300 mM DHPC, 20 mM NaH2PO4, 100 mM NaCl.

#	Name	Isotope labeling	Concentration
7	KpOmpA transmembrane domain	[U-13C; U-15N; U-2H]/[L,V,I(delta1)-13CH3]	1 mM
8	DHPC		300 mM
9	NaH2PO4		20 mM
10	NaCl		100 mM
11	H2O	natural abundance	90 %
12	D2O		10 %

8 3D H(CCCO)-TOCSY

Instrument

Bruker Avance - 500 MHz Four radio-frequency 1H, 2H, 13C, 15N channels, 1H-{13C, 15N}-triple resonance cryoprobe, z-gradient coil.

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 6.5, Details 1mM protein, 300 mM DHPC, 20 mM NaH2PO4, 100 mM NaCl.

#	Name	Isotope labeling	Concentration
7	KpOmpA transmembrane domain	[U-13C; U-15N; U-2H]/[L,V,I(delta1)-13CH3]	1 mM
8	DHPC		300 mM
9	NaH2PO4		20 mM
10	NaCl		100 mM
11	H2O	natural abundance	90 %
12	D2O		10 %

9 2D [1H,13C]-CT-HSQC

Instrument

Bruker Avance - 700 MHz Three radio-frequency 1H, 13C, 15N channels, 1H-{13C, 15N}-triple resonance probe, z-gradient coil.

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 6.5, Details 1mM protein, 300 mM DHPC(d22), 20 mM NaH2PO4, 100 mM NaCl.

#	Name	Isotope labeling	Concentration
13	KpOmpA transmembrane domain	[U-15N; 10% 13C]	1 mM
14	DHPC		300 mM
15	NaH2PO4		20 mM
16	NaCl		100 mM
17	H2O	natural abundance	90 %
18	D2O		10 %

10 4D 15N,15N-separated HMQC-NOESY-TROSY

Instrument

Bruker Avance - 800 MHz Four radio-frequency 1H, 2H, 13C, 15N channels, 1H-{13C, 15N}-triple resonance cryoprobe, z-gradient coil.

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 6.5, Details 1mM protein, 300 mM DHPC, 20 mM NaH2PO4, 100 mM NaCl.

#	Name	Isotope labeling	Concentration
1	KpOmpA transmembrane domain	[U-13C; U-15N; U-2H]	1 mM
2	DHPC		300 mM
3	NaH2PO4		20 mM
4	NaCl		100 mM
5	H2O	natural abundance	90 %
6	D2O		10 %

11 3D 15N,13C-separated HMQC-NOESY-TROSY

Instrument

Bruker Avance - 900 MHz Four radio-frequency 1H, 2H, 13C, 15N channels, 1H-{13C, 15N}-triple resonance cryoprobe, z-gradient coil.

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 6.5, Details 1mM protein, 300 mM DHPC(d22), 20 mM NaH2PO4, 100 mM NaCl.

#	Name	Isotope labeling	Concentration
19	KpOmpA transmembrane domain	[U-13C; U-15N; U-2H]/[L,V,I(delta1)-13CH3]	1 mM
20	DHPC		300 mM
21	NaH2PO4		20 mM
22	NaCl		100 mM
23	H2O	natural abundance	90 %
24	D2O		10 %

12 3D 13C,13C-separated HMQC-NOESY

Instrument

Bruker Avance - 900 MHz Four radio-frequency 1H, 2H, 13C, 15N channels, 1H-{13C, 15N}-triple resonance cryoprobe, z-gradient coil.

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 6.5, Details 1mM protein, 300 mM DHPC(d22), 20 mM NaH2PO4, 100 mM NaCl.

#	Name	Isotope labeling	Concentration
19	KpOmpA transmembrane domain	[U-13C; U-15N; U-2H]/[L,V,I(delta1)-13CH3]	1 mM
20	DHPC		300 mM
21	NaH2PO4		20 mM
22	NaCl		100 mM
23	H2O	natural abundance	90 %
24	D2O		10 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15651_2k0l.nef
Input source #2: Coordindates	2k0l.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

None

Sequence alignments

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

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

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

-------210------
VAPAPAPAPEHHHHHH
||||||||||||||||
VAPAPAPAPEHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	216	0	0	100.0

Content subtype: combined_15651_2k0l.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	Assignment_KpOmpA	Warning	1076		87.0 (chain: A, length: 216)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	528 (1)	noe	59.3 (chain: A, length: 216)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	128 (1)	hbond	29.6 (chain: A, length: 216)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	264 (264)	.	91.2 (chain: A, length: 216)

Assigned chemical shifts

Saveframe: Assignment_KpOmpA
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 216, Sequence coverage: 87.0%
- Total number of assignments
  - ¹³C chemical shifts: 673
  - ¹H chemical shifts: 233
  - ¹⁵N chemical shifts: 170
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
44	ASN	CG	179.178
86	ASN	CG	179.062

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	934	671	71.8
¹H chemical shifts	1229	233	19.0
¹⁵N chemical shifts	242	170	70.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	432	373	86.3
¹H chemical shifts	452	168	37.2
¹⁵N chemical shifts	205	168	82.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	502	298	59.4
¹H chemical shifts	777	65	8.4
¹⁵N chemical shifts	37	2	5.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	106	98	92.5
¹H chemical shifts	106	63	59.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	134	0	0.0
¹H chemical shifts	140	2	1.4
¹⁵N chemical shifts	6	2	33.3

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 216, Sequence coverage: 59.3%
- Total number of restraints: 528
- Weight of restraints: 1.0 (528)
- Potential type of restraints: square-well-parabolic (528)
- Range of distance target values: 3.0, 8.0 (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: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 216, Sequence coverage: 29.6%
  - Total number of restraints: 128
  - Weight of restraints: 1.0 (128)
  - Potential type of restraints: square-well-parabolic (128)
  - Range of distance target values: 1.7, 3.0 (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_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 216, Sequence coverage: 91.2%
- Total number of restraints: 264
- Total number of restraints per polymer type: 264
- Weight of restraints: 1.0 (264)
- Potential type of restraints: square-well-parabolic (264)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords 4D NOESY, CC-TOCSY, conformational exchange, membrane protein, methyl protonation, Outer membrane protein A, side-chains assignment, TROSY, DHPC micelles, OMPA, Sidechain

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.886 seconds)

BMRB: 15651

Sample #1

Sample #2

Sample #3

Sample #4

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. KpOmpA transmembrane domain, : 1 : 1 : 24 entities Detail

Experiments performed 12 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail