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BMRB: 25030

2MQE

Solution structure of Escherichia coli Outer membrane protein A C-terminal domain

Authors

Ishida, H., Vogel, H.

Assembly

OMPA C-terminal domain

Entity

1. OMPA C-terminal domain (polymer), 146 monomers, 15694.51 Da Detail

APAPAPAPEV QTKHFTLKSD VLFNFNKATL KPEGQAALDQ LYSQLSNLDP KDGSVVVLGY TDRIGSDAYN QGLSERRAQS VVDYLISKGI PADKISARGM GESNPVTGNT CDNVKQRAAL IDCLAPDRRV EIEVKGIKDV VTQPQA

Formula weight

15694.51 Da

Source organism

Escherichia coli

Exptl. method

Refine. method

torsion angle dynamics, simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 88.4 %, Completeness: 28.9 %, Completeness (bb): 62.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹⁵N
All	28.9 % (290 of 1004)	18.9 % (161 of 852)	84.9 % (129 of 152)
Backbone	62.1 % (266 of 428)	47.3 % (138 of 292)	94.1 % (128 of 136)
Sidechain	4.2 % (24 of 576)	4.1 % (23 of 560)	6.3 % (1 of 16)
Aromatic	0.0 % (0 of 33)	0.0 % (0 of 33)
Methyl	8.1 % (7 of 86)	8.1 % (7 of 86)

1. entity

APAPAPAPEV QTKHFTLKSD VLFNFNKATL KPEGQAALDQ LYSQLSNLDP KDGSVVVLGY TDRIGSDAYN QGLSERRAQS VVDYLISKGI PADKISARGM GESNPVTGNT CDNVKQRAAL IDCLAPDRRV EIEVKGIKDV VTQPQA

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 15N]		0.5 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium azide	natural abundance		0.03 %
4	DSS	natural abundance		0.5 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
5	entity	[U-100% 13C; U-100% 15N]		0.5 mM
6	sodium phosphate	natural abundance		20 mM
7	sodium azide	natural abundance		0.03 %
8	DSS	natural abundance		0.5 mM

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
9	entity	[U-100% 13C; U-100% 15N]		0.5 mM
10	sodium phosphate	natural abundance		20 mM
11	sodium azide	natural abundance		0.03 %
12	DSS	natural abundance		0.5 mM

Protein Blocks Logo

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

Release date

2014-09-01

Citation

The periplasmic domain of Escherichia coli outer membrane protein A can undergo a localized temperature dependent structural transition
Ishida, H., Garcia-Herrero, A., Vogel, H.
Biochim. Biophys. Acta (2014), 1838, 3014-3024, PubMed 25135663 , DOI 10.1016/j.bbamem.2014.08.008 , Abstract

Related entities 1. OMPA C-terminal domain, : 1 : 5 : 2 : 66 entities Detail

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 15N]		0.5 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium azide	natural abundance		0.03 %
4	DSS	natural abundance		0.5 mM

2 3D HNCACB

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
5	entity	[U-100% 13C; U-100% 15N]		0.5 mM
6	sodium phosphate	natural abundance		20 mM
7	sodium azide	natural abundance		0.03 %
8	DSS	natural abundance		0.5 mM

3 3D CBCA(CO)NH

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
5	entity	[U-100% 13C; U-100% 15N]		0.5 mM
6	sodium phosphate	natural abundance		20 mM
7	sodium azide	natural abundance		0.03 %
8	DSS	natural abundance		0.5 mM

4 3D HNCO

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
5	entity	[U-100% 13C; U-100% 15N]		0.5 mM
6	sodium phosphate	natural abundance		20 mM
7	sodium azide	natural abundance		0.03 %
8	DSS	natural abundance		0.5 mM

5 3D HN(CA)CO

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
5	entity	[U-100% 13C; U-100% 15N]		0.5 mM
6	sodium phosphate	natural abundance		20 mM
7	sodium azide	natural abundance		0.03 %
8	DSS	natural abundance		0.5 mM

6 3D HBHA(CO)NH

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
5	entity	[U-100% 13C; U-100% 15N]		0.5 mM
6	sodium phosphate	natural abundance		20 mM
7	sodium azide	natural abundance		0.03 %
8	DSS	natural abundance		0.5 mM

7 3D H(CCO)NH

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
5	entity	[U-100% 13C; U-100% 15N]		0.5 mM
6	sodium phosphate	natural abundance		20 mM
7	sodium azide	natural abundance		0.03 %
8	DSS	natural abundance		0.5 mM

8 3D C(CO)NH

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
5	entity	[U-100% 13C; U-100% 15N]		0.5 mM
6	sodium phosphate	natural abundance		20 mM
7	sodium azide	natural abundance		0.03 %
8	DSS	natural abundance		0.5 mM

9 3D 1H-15N NOESY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
5	entity	[U-100% 13C; U-100% 15N]		0.5 mM
6	sodium phosphate	natural abundance		20 mM
7	sodium azide	natural abundance		0.03 %
8	DSS	natural abundance		0.5 mM

10 3D 1H-13C NOESY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
9	entity	[U-100% 13C; U-100% 15N]		0.5 mM
10	sodium phosphate	natural abundance		20 mM
11	sodium azide	natural abundance		0.03 %
12	DSS	natural abundance		0.5 mM

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_25030_2mqe.nef
Input source #2: Coordindates	2mqe.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:290:CYS:SG	A:302:CYS:SG	unknown	unknown	2.019

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

180-----190-------200-------210-------220-------230-------240-------250-------260-------270-------28
APAPAPAPEVQTKHFTLKSDVLFNFNKATLKPEGQAALDQLYSQLSNLDPKDGSVVVLGYTDRIGSDAYNQGLSERRAQSVVDYLISKGIPADKISARGM
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
APAPAPAPEVQTKHFTLKSDVLFNFNKATLKPEGQAALDQLYSQLSNLDPKDGSVVVLGYTDRIGSDAYNQGLSERRAQSVVDYLISKGIPADKISARGM
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

0-------290-------300-------310-------320-----
GESNPVTGNTCDNVKQRAALIDCLAPDRRVEIEVKGIKDVVTQPQA
||||||||||||||||||||||||||||||||||||||||||||||
GESNPVTGNTCDNVKQRAALIDCLAPDRRVEIEVKGIKDVVTQPQA
-------110-------120-------130-------140------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	146	0	0	100.0

Content subtype: combined_25030_2mqe.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	OK	254		87.0 (chain: A, length: 146)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	2296 (1)	noe	93.8 (chain: A, length: 146)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	100 (1)	hbond	46.6 (chain: A, length: 146)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	258 (258)	.	93.2 (chain: A, length: 146)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_5	OK	99 (99)	.	67.8 (chain: A, length: 146)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 146, Sequence coverage: 87.0%
- Total number of assignments
  - ¹H chemical shifts: 127
  - ¹⁵N chemical shifts: 127
- 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

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: 146, Sequence coverage: 93.8%
- Total number of restraints: 2290
- Weight of restraints: 1.0 (2290)
- Potential type of restraints: square-well-parabolic (2290)
- Range of distance target values: 1.1, 3.0 (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: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 146, Sequence coverage: 46.6%
  - Total number of restraints: 100
  - Weight of restraints: 1.0 (100)
  - Potential type of restraints: square-well-parabolic (100)
  - Range of distance target values: 1.0, 1.5 (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: 146, Sequence coverage: 93.2%
- Total number of restraints: 258
- Total number of restraints per polymer type: 258
- Weight of restraints: 1.0 (258)
- Potential type of restraints: square-well-parabolic (258)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_5

Status: OK
Experiment type: .

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 146, Sequence coverage: 67.8%

180-----190-------200-------210-------220-------230-------240-------250-------260-------270-------28
APAPAPAPEVQTKHFTLKSDVLFNFNKATLKPEGQAALDQLYSQLSNLDPKDGSVVVLGYTDRIGSDAYNQGLSERRAQSVVDYLISKGIPADKISARGM
         ||||||||| |||| ||  ||| ||| | |||||||| |  | |||||||||   ||||    ||||   ||||||| ||| || || |||
.........VQTKHFTLK.DVLF.FN..TLK.EGQ.A.DQLYSQLS.L..K.GSVVVLGYT...GSDA....LSER...SVVDYLI.KGI.AD.IS.RGM

0-------290-------300-------310-------320-----
GESNPVTGNTCDNVKQRAALIDCLAPDRRVEIEVKGIKDVVTQPQA
|  | ||||||||| || || | || |||||||||| |||  |  |
G..N.VTGNTCDNV.QR.AL.D.LA.DRRVEIEVKG.KDV..Q..A

Total number of restraints: 99
Potential type of restraints: undefined (99)
Range of observed RDC values: 100.0, -100.0 (Hz)
RDC restraints per residue
- Chain_ID: A
  None

Keywords Outer membrane protein A, OmpA, Escherichia coli