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BMRB: 16926

2KXX

NMR Structure of Escherichia coli BamE, a Lipoprotein Component of the beta-Barrel Assembly Machinery Complex

Authors

Kim, K., Okon, M., Escobar, E., Kang, H., McIntosh, L., Paetzel, M.

Assembly

E. coli lipoprotein

Entity

1. E. coli lipoprotein (polymer, Thiol state: not present), 97 monomers, 10693.81 Da Detail

GSHMSTLERV VYRPDINQGN YLTANDVSKI RVGMTQQQVA YALGTPLMSD PFGTNTWFYV FRQQPGHEGV TQQTLTLTFN SSGVLTNIDN KPALSGN

Formula weight

10693.81 Da

Source organism

Escherichia coli

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 92.8 %, Completeness: 71.0 %, Completeness (bb): 71.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	71.0 % (785 of 1106)	77.2 % (440 of 570)	58.5 % (250 of 427)	87.2 % (95 of 109)
Backbone	71.0 % (406 of 572)	88.9 % (176 of 198)	51.8 % (146 of 282)	91.3 % (84 of 92)
Sidechain	73.5 % (457 of 622)	71.0 % (264 of 372)	78.1 % (182 of 233)	64.7 % (11 of 17)
Aromatic	41.3 % (38 of 92)	41.3 % (19 of 46)	40.0 % (18 of 45)	100.0 % (1 of 1)
Methyl	89.6 % (95 of 106)	86.8 % (46 of 53)	92.5 % (49 of 53)

1. E. coli lipoprotein

GSHMSTLERV VYRPDINQGN YLTANDVSKI RVGMTQQQVA YALGTPLMSD PFGTNTWFYV FRQQPGHEGV TQQTLTLTFN SSGVLTNIDN KPALSGN

Show sample condition

Sample

Solvent system 85% H2O/15% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6

#	Name	Isotope labeling	Type	Concentration
1	E. coli protein	[U-100% 13C; U-100% 15N]		0.5 mM
2	D2O	natural abundance		15 %
3	H2O	natural abundance		85 %
4	Na2HPO4/NaH2PO4	natural abundance		20 mM

LACS Plot; CA

Referencing offset: -0.04 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: -0.04 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: 0.08 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2011-01-05

Citation

Structural characterization of Escherichia coli BamE, a lipoprotein component of the β-barrel assembly machinery complex
Kim, K.H., Kang, H., Okon, M., Escobar-Cabrera, E., McIntosh, L.P., Paetzel, M.
Biochemistry (2011), 50, 1081-1090, PubMed 21207987 , DOI 10.1021/bi101659u , Abstract

Related entities 1. E. coli lipoprotein, : 1 : 77 : 19 entities Detail

Experiments performed 8 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian Unity - 500 MHz

Sample

State isotropic, Solvent system 85% H2O/15% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6

#	Name	Isotope labeling	Type	Concentration
1	E. coli protein	[U-100% 13C; U-100% 15N]		0.5 mM
2	D2O	natural abundance		15 %
3	H2O	natural abundance		85 %
4	Na2HPO4/NaH2PO4	natural abundance		20 mM

2 3D CBCA(CO)NH

Instrument

Varian Unity - 500 MHz

Sample

State isotropic, Solvent system 85% H2O/15% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6

#	Name	Isotope labeling	Type	Concentration
1	E. coli protein	[U-100% 13C; U-100% 15N]		0.5 mM
2	D2O	natural abundance		15 %
3	H2O	natural abundance		85 %
4	Na2HPO4/NaH2PO4	natural abundance		20 mM

3 3D 1H-15N NOESY

Instrument

Varian Unity - 500 MHz

Sample

State isotropic, Solvent system 85% H2O/15% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6

#	Name	Isotope labeling	Type	Concentration
1	E. coli protein	[U-100% 13C; U-100% 15N]		0.5 mM
2	D2O	natural abundance		15 %
3	H2O	natural abundance		85 %
4	Na2HPO4/NaH2PO4	natural abundance		20 mM

4 3D HNCO

Instrument

Varian Unity - 500 MHz

Sample

State isotropic, Solvent system 85% H2O/15% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6

#	Name	Isotope labeling	Type	Concentration
1	E. coli protein	[U-100% 13C; U-100% 15N]		0.5 mM
2	D2O	natural abundance		15 %
3	H2O	natural abundance		85 %
4	Na2HPO4/NaH2PO4	natural abundance		20 mM

5 3D HNCACB

Instrument

Varian Unity - 500 MHz

Sample

State isotropic, Solvent system 85% H2O/15% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6

#	Name	Isotope labeling	Type	Concentration
1	E. coli protein	[U-100% 13C; U-100% 15N]		0.5 mM
2	D2O	natural abundance		15 %
3	H2O	natural abundance		85 %
4	Na2HPO4/NaH2PO4	natural abundance		20 mM

6 3D HN(CO)CA

Instrument

Varian Unity - 500 MHz

Sample

State isotropic, Solvent system 85% H2O/15% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6

#	Name	Isotope labeling	Type	Concentration
1	E. coli protein	[U-100% 13C; U-100% 15N]		0.5 mM
2	D2O	natural abundance		15 %
3	H2O	natural abundance		85 %
4	Na2HPO4/NaH2PO4	natural abundance		20 mM

7 3D 1H-13C NOESY

Instrument

Varian Unity - 500 MHz

Sample

State isotropic, Solvent system 85% H2O/15% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6

#	Name	Isotope labeling	Type	Concentration
1	E. coli protein	[U-100% 13C; U-100% 15N]		0.5 mM
2	D2O	natural abundance		15 %
3	H2O	natural abundance		85 %
4	Na2HPO4/NaH2PO4	natural abundance		20 mM

8 2D 1H-1H COSY

Instrument

Varian Unity - 500 MHz

Sample

State isotropic, Solvent system 85% H2O/15% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6

#	Name	Isotope labeling	Type	Concentration
1	E. coli protein	[U-100% 13C; U-100% 15N]		0.5 mM
2	D2O	natural abundance		15 %
3	H2O	natural abundance		85 %
4	Na2HPO4/NaH2PO4	natural abundance		20 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_16926_2kxx.nef
Input source #2: Coordindates	2kxx.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

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

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	97	0	0	100.0

Content subtype: combined_16926_2kxx.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list	Warning	772		90.7 (chain: A, length: 97)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	20 (1)	hbond	10.3 (chain: A, length: 97)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	98 (98)	.	68.0 (chain: A, length: 97)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 97, Sequence coverage: 90.7%
- Total number of assignments
  - ¹H chemical shifts: 444
  - ¹³C chemical shifts: 236
  - ¹⁵N chemical shifts: 92
- 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

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_3
- Status: Warning
- Experiment type: hbond
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 97, Sequence coverage: 10.3%
- Total number of restraints: 20
- Weight of restraints: 1.0 (20)
- Potential type of restraints: upper-bound-parabolic (20)
- Range of distance target values: 1.8, 2.7 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 97, Sequence coverage: 68.0%
- Total number of restraints: 98
- Total number of restraints per polymer type: 98
- Weight of restraints: 1.0 (98)
- Potential type of restraints: square-well-parabolic (98)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords E coli protein, lipoprotein