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BMRB: 18332

2LQV

E. coli Protein

Authors

Prehna, G., Zhang, G., Gong, X., Duszyk, M., Okon, M., McIntosh, L.P., Weiner, J.H., Strynadka, N.CJ.

Assembly

Escherichia coli Porins

Entity

1. Escherichia coli Porins (polymer), 99 monomers, 11039.17 Da Detail

ANNETSKSVT FPKCEDLDAA GIAASVKRDY QQNRVARWAD DQKIVGQADP VAWVSLQDIQ GKDDKWSVPL TVRGKSADIH YQVSVDCKAG MAEYQRRLE

Formula weight

11039.17 Da

Entity Connection

disulfide 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS14:SG	1:CYS87:SG

Source organism

Escherichia coli

Exptl. method

Refine. method

distance geometry, simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 77.8 %, Completeness: 62.0 %, Completeness (bb): 62.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	62.0 % (698 of 1125)	65.4 % (383 of 586)	57.6 % (247 of 429)	61.8 % (68 of 110)
Backbone	62.1 % (365 of 588)	68.0 % (136 of 200)	56.5 % (165 of 292)	66.7 % (64 of 96)
Sidechain	63.2 % (399 of 631)	64.0 % (247 of 386)	64.1 % (148 of 231)	28.6 % (4 of 14)
Aromatic	52.7 % (39 of 74)	54.1 % (20 of 37)	50.0 % (17 of 34)	66.7 % (2 of 3)
Methyl	75.5 % (77 of 102)	76.5 % (39 of 51)	74.5 % (38 of 51)

1. E coli protein

ANNETSKSVT FPKCEDLDAA GIAASVKRDY QQNRVARWAD DQKIVGQADP VAWVSLQDIQ GKDDKWSVPL TVRGKSADIH YQVSVDCKAG MAEYQRRLE

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 50 mM HEPES pH 6.5 100 mM NaCl 0.1 mM TCEP 0.1 mM PMSF

#	Name	Isotope labeling	Type	Concentration
1	E coli protein	[U-100% 13C; U-100% 15N]		0.5 ~ 1.0 mM
2	HEPES	natural abundance		50 mM
3	sodium chloride	natural abundance		100 mM
4	TCEP	natural abundance		0.1 mM
5	PMSF	natural abundance		0.1 mM
6	H2O	natural abundance		95 %
7	D2O	natural abundance		5 %

LACS Plot; CA

Referencing offset: 0.25 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: 0.25 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: -0.09 ppm, Outliers: 3 Detail

Protein Blocks Logo

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

Release date

2012-06-04

Citation

A protein export pathway involving Escherichia coli porins
Prehna, G., Zhang, G., Gong, X., Duszyk, M., Okon, M., McIntosh, L.P., Weiner, J.H., Strynadka, N.C.J.
Structure (2012), 20, 1154-1166, PubMed 22658749 , DOI 10.1016/j.str.2012.04.014 , Abstract

Related entities 1. Escherichia coli Porins, : 1 : 5 : 4 entities Detail

Experiments performed 13 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian Unity - 500 MHz cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 50 mM HEPES pH 6.5 100 mM NaCl 0.1 mM TCEP 0.1 mM PMSF

#	Name	Isotope labeling	Type	Concentration
1	E coli protein	[U-100% 13C; U-100% 15N]		0.5 ~ 1.0 mM
2	HEPES	natural abundance		50 mM
3	sodium chloride	natural abundance		100 mM
4	TCEP	natural abundance		0.1 mM
5	PMSF	natural abundance		0.1 mM
6	H2O	natural abundance		95 %
7	D2O	natural abundance		5 %

2 3D CBCA(CO)NH

Instrument

Varian Unity - 500 MHz cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 50 mM HEPES pH 6.5 100 mM NaCl 0.1 mM TCEP 0.1 mM PMSF

#	Name	Isotope labeling	Type	Concentration
1	E coli protein	[U-100% 13C; U-100% 15N]		0.5 ~ 1.0 mM
2	HEPES	natural abundance		50 mM
3	sodium chloride	natural abundance		100 mM
4	TCEP	natural abundance		0.1 mM
5	PMSF	natural abundance		0.1 mM
6	H2O	natural abundance		95 %
7	D2O	natural abundance		5 %

3 3D HNCACB

Instrument

Varian Unity - 500 MHz cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 50 mM HEPES pH 6.5 100 mM NaCl 0.1 mM TCEP 0.1 mM PMSF

#	Name	Isotope labeling	Type	Concentration
1	E coli protein	[U-100% 13C; U-100% 15N]		0.5 ~ 1.0 mM
2	HEPES	natural abundance		50 mM
3	sodium chloride	natural abundance		100 mM
4	TCEP	natural abundance		0.1 mM
5	PMSF	natural abundance		0.1 mM
6	H2O	natural abundance		95 %
7	D2O	natural abundance		5 %

4 3D HNCO

Instrument

Varian Unity - 500 MHz cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 50 mM HEPES pH 6.5 100 mM NaCl 0.1 mM TCEP 0.1 mM PMSF

#	Name	Isotope labeling	Type	Concentration
1	E coli protein	[U-100% 13C; U-100% 15N]		0.5 ~ 1.0 mM
2	HEPES	natural abundance		50 mM
3	sodium chloride	natural abundance		100 mM
4	TCEP	natural abundance		0.1 mM
5	PMSF	natural abundance		0.1 mM
6	H2O	natural abundance		95 %
7	D2O	natural abundance		5 %

5 3D HCACO

Instrument

Varian Unity - 500 MHz cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 50 mM HEPES pH 6.5 100 mM NaCl 0.1 mM TCEP 0.1 mM PMSF

#	Name	Isotope labeling	Type	Concentration
1	E coli protein	[U-100% 13C; U-100% 15N]		0.5 ~ 1.0 mM
2	HEPES	natural abundance		50 mM
3	sodium chloride	natural abundance		100 mM
4	TCEP	natural abundance		0.1 mM
5	PMSF	natural abundance		0.1 mM
6	H2O	natural abundance		95 %
7	D2O	natural abundance		5 %

6 3D HCCH-TOCSY

Instrument

Varian Unity - 500 MHz cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 50 mM HEPES pH 6.5 100 mM NaCl 0.1 mM TCEP 0.1 mM PMSF

#	Name	Isotope labeling	Type	Concentration
1	E coli protein	[U-100% 13C; U-100% 15N]		0.5 ~ 1.0 mM
2	HEPES	natural abundance		50 mM
3	sodium chloride	natural abundance		100 mM
4	TCEP	natural abundance		0.1 mM
5	PMSF	natural abundance		0.1 mM
6	H2O	natural abundance		95 %
7	D2O	natural abundance		5 %

7 3D 1H-15N NOESY

Instrument

Varian Unity - 500 MHz cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 50 mM HEPES pH 6.5 100 mM NaCl 0.1 mM TCEP 0.1 mM PMSF

#	Name	Isotope labeling	Type	Concentration
1	E coli protein	[U-100% 13C; U-100% 15N]		0.5 ~ 1.0 mM
2	HEPES	natural abundance		50 mM
3	sodium chloride	natural abundance		100 mM
4	TCEP	natural abundance		0.1 mM
5	PMSF	natural abundance		0.1 mM
6	H2O	natural abundance		95 %
7	D2O	natural abundance		5 %

8 3D 1H-13C NOESY

Instrument

Varian Unity - 500 MHz cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 50 mM HEPES pH 6.5 100 mM NaCl 0.1 mM TCEP 0.1 mM PMSF

#	Name	Isotope labeling	Type	Concentration
1	E coli protein	[U-100% 13C; U-100% 15N]		0.5 ~ 1.0 mM
2	HEPES	natural abundance		50 mM
3	sodium chloride	natural abundance		100 mM
4	TCEP	natural abundance		0.1 mM
5	PMSF	natural abundance		0.1 mM
6	H2O	natural abundance		95 %
7	D2O	natural abundance		5 %

9 CCC-TOCSY-NNH

Instrument

Varian Unity - 500 MHz cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 50 mM HEPES pH 6.5 100 mM NaCl 0.1 mM TCEP 0.1 mM PMSF

#	Name	Isotope labeling	Type	Concentration
1	E coli protein	[U-100% 13C; U-100% 15N]		0.5 ~ 1.0 mM
2	HEPES	natural abundance		50 mM
3	sodium chloride	natural abundance		100 mM
4	TCEP	natural abundance		0.1 mM
5	PMSF	natural abundance		0.1 mM
6	H2O	natural abundance		95 %
7	D2O	natural abundance		5 %

10 HCC-TOCSY-NNH

Instrument

Varian Unity - 500 MHz cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 50 mM HEPES pH 6.5 100 mM NaCl 0.1 mM TCEP 0.1 mM PMSF

#	Name	Isotope labeling	Type	Concentration
1	E coli protein	[U-100% 13C; U-100% 15N]		0.5 ~ 1.0 mM
2	HEPES	natural abundance		50 mM
3	sodium chloride	natural abundance		100 mM
4	TCEP	natural abundance		0.1 mM
5	PMSF	natural abundance		0.1 mM
6	H2O	natural abundance		95 %
7	D2O	natural abundance		5 %

11 (HB)CB(CGCD)HD-aromatic

Instrument

Varian Unity - 500 MHz cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 50 mM HEPES pH 6.5 100 mM NaCl 0.1 mM TCEP 0.1 mM PMSF

#	Name	Isotope labeling	Type	Concentration
1	E coli protein	[U-100% 13C; U-100% 15N]		0.5 ~ 1.0 mM
2	HEPES	natural abundance		50 mM
3	sodium chloride	natural abundance		100 mM
4	TCEP	natural abundance		0.1 mM
5	PMSF	natural abundance		0.1 mM
6	H2O	natural abundance		95 %
7	D2O	natural abundance		5 %

12 HBGCBGCCBGCACONNH

Instrument

Varian Unity - 500 MHz cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 50 mM HEPES pH 6.5 100 mM NaCl 0.1 mM TCEP 0.1 mM PMSF

#	Name	Isotope labeling	Type	Concentration
1	E coli protein	[U-100% 13C; U-100% 15N]		0.5 ~ 1.0 mM
2	HEPES	natural abundance		50 mM
3	sodium chloride	natural abundance		100 mM
4	TCEP	natural abundance		0.1 mM
5	PMSF	natural abundance		0.1 mM
6	H2O	natural abundance		95 %
7	D2O	natural abundance		5 %

13 CT-HSQC

Instrument

Varian Unity - 500 MHz cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5, Details 50 mM HEPES pH 6.5 100 mM NaCl 0.1 mM TCEP 0.1 mM PMSF

#	Name	Isotope labeling	Type	Concentration
1	E coli protein	[U-100% 13C; U-100% 15N]		0.5 ~ 1.0 mM
2	HEPES	natural abundance		50 mM
3	sodium chloride	natural abundance		100 mM
4	TCEP	natural abundance		0.1 mM
5	PMSF	natural abundance		0.1 mM
6	H2O	natural abundance		95 %
7	D2O	natural abundance		5 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_18332_2lqv.nef
Input source #2: Coordindates	2lqv.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:35:CYS:SG	A:108:CYS:SG	oxidized, CA 54.045, CB 40.904 ppm	oxidized, CA 57.07, CB 40.994 ppm	2.038

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

-------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-
ANNETSKSVTFPKCEDLDAAGIAASVKRDYQQNRVARWADDQKIVGQADPVAWVSLQDIQGKDDKWSVPLTVRGKSADIHYQVSVDCKAGMAEYQRRLEH
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ANNETSKSVTFPKCEDLDAAGIAASVKRDYQQNRVARWADDQKIVGQADPVAWVSLQDIQGKDDKWSVPLTVRGKSADIHYQVSVDCKAGMAEYQRRLEH
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-----
HHHHH
|||||
HHHHH
-----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	105	0	0	100.0

Content subtype: combined_18332_2lqv.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	688		70.5 (chain: A, length: 105)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	1512 (1)	noe	67.6 (chain: A, length: 105)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	44 (1)	hbond	31.4 (chain: A, length: 105)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 105, Sequence coverage: 70.5%
- Total number of assignments
  - ¹H chemical shifts: 382
  - ¹³C chemical shifts: 239
  - ¹⁵N chemical shifts: 67
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 105, Sequence coverage: 67.6%
- Total number of restraints: 1512
- Weight of restraints: 1.0 (1512)
- Potential type of restraints: square-well-parabolic (1512)
- Range of distance target values: 1.09, 2.75 (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: 105, Sequence coverage: 31.4%
  - Total number of restraints: 44
  - Weight of restraints: 1.0 (44)
  - Potential type of restraints: square-well-parabolic (44)
  - Range of distance target values: 2.0, 2.95 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Keywords E. coli, Secretion