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Found 1 Document (0.704 seconds)

BMRB: 25869

2N8X

Solution structure of LptE from Pseudomonas Aerigunosa

Authors

Moehle, K., Kocherla, H., Jurt, S., Robinson, J., Zerbe, O., Zerbe, K., Bacsa, B.

Assembly

LptE

Entity

1. LptE (polymer, Thiol state: all free), 166 monomers, 18391.27 Da Detail

GTSGFQLRGL GDAQFALKEI DVSARNAYGP TVRELKETLE NSGVKVTSNA PYHLVLVRED NQQRTVSYTG SARGAEFELT NTINYEIVGA NDLVLMSNQV QVQKVYVHDE NNLIGSDQEA AQLRSEMRRD LIQQLSMRLQ ALTPAQLDEA QRQAEAKAKA EAEALR

Formula weight

18391.27 Da

Source organism

Pseudomonas aeruginosa

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.8 %, Completeness: 85.2 %, Completeness (bb): 91.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	85.2 % (1604 of 1883)	85.4 % (837 of 980)	83.6 % (598 of 715)	89.9 % (169 of 188)
Backbone	91.6 % (907 of 990)	96.2 % (326 of 339)	86.9 % (424 of 488)	96.3 % (157 of 163)
Sidechain	80.2 % (841 of 1049)	79.7 % (511 of 641)	83.0 % (318 of 383)	48.0 % (12 of 25)
Aromatic	73.1 % (57 of 78)	79.5 % (31 of 39)	66.7 % (26 of 39)
Methyl	97.0 % (194 of 200)	99.0 % (99 of 100)	95.0 % (95 of 100)

1. entity

GTSGFQLRGL GDAQFALKEI DVSARNAYGP TVRELKETLE NSGVKVTSNA PYHLVLVRED NQQRTVSYTG SARGAEFELT NTINYEIVGA NDLVLMSNQV QVQKVYVHDE NNLIGSDQEA AQLRSEMRRD LIQQLSMRLQ ALTPAQLDEA QRQAEAKAKA EAEALR

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5, Details 0.45 mM 15N-labeled LptE

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	50 mM
2	sodium chloride	natural abundance	25 mM
3	CHAPS	natural abundance	20 mM
4	LptE	15N-labeled	0.45 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5, Details 0.35 mM 15N,13C-labeled LptE

#	Name	Isotope labeling	Concentration
7	sodium phosphate	natural abundance	50 mM
8	sodium chloride	natural abundance	25 mM
9	CHAPS	natural abundance	20 mM
10	LptE	15N,13C-labeled	0.35 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5, Details 0.35 mM 2H,15N,13C-labeled LptE

#	Name	Isotope labeling	Concentration
13	sodium phosphate	natural abundance	50 mM
14	sodium chloride	natural abundance	25 mM
15	LptE	2H,15N,13C-labeled	0.35 mM
16	H2O	natural abundance	90 %
17	D2O	natural abundance	10 %

LACS Plot; CA

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

Referencing offset: 0.19 ppm, Outliers: 2 Detail

LACS Plot; CB

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

Referencing offset: 0.19 ppm, Outliers: 2 Detail

LACS Plot; HA

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

Referencing offset: 0.02 ppm, Outliers: 1 Detail

LACS Plot; CO

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

Referencing offset: 0.17 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2N8X, Strand ID: A Detail

Release date

2016-05-22

Citation

Solution Structure and Dynamics of LptE from Pseudomonas aeruginosa
Moehle, K., Kocherla, H., Bacsa, B., Zerbe, K., Robinson, J., Zerbe, O.
Biochemistry (2016), 55, 2936-2943, PubMed 27166502 , DOI 10.1021/acs.biochem.6b00313 , Abstract

Related entities 1. LptE, : 1 : 1 : 9 entities Detail

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5, Details 0.45 mM 15N-labeled LptE

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	50 mM
2	sodium chloride	natural abundance	25 mM
3	CHAPS	natural abundance	20 mM
4	LptE	15N-labeled	0.45 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

2 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5, Details 0.35 mM 15N,13C-labeled LptE

#	Name	Isotope labeling	Concentration
7	sodium phosphate	natural abundance	50 mM
8	sodium chloride	natural abundance	25 mM
9	CHAPS	natural abundance	20 mM
10	LptE	15N,13C-labeled	0.35 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

3 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5, Details 0.35 mM 15N,13C-labeled LptE

#	Name	Isotope labeling	Concentration
7	sodium phosphate	natural abundance	50 mM
8	sodium chloride	natural abundance	25 mM
9	CHAPS	natural abundance	20 mM
10	LptE	15N,13C-labeled	0.35 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

4 3D HNCO

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5, Details 0.35 mM 2H,15N,13C-labeled LptE

#	Name	Isotope labeling	Concentration
13	sodium phosphate	natural abundance	50 mM
14	sodium chloride	natural abundance	25 mM
15	LptE	2H,15N,13C-labeled	0.35 mM
16	H2O	natural abundance	90 %
17	D2O	natural abundance	10 %

5 3D HNCACB

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5, Details 0.35 mM 2H,15N,13C-labeled LptE

#	Name	Isotope labeling	Concentration
13	sodium phosphate	natural abundance	50 mM
14	sodium chloride	natural abundance	25 mM
15	LptE	2H,15N,13C-labeled	0.35 mM
16	H2O	natural abundance	90 %
17	D2O	natural abundance	10 %

6 3D HN(CO)CACB

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5, Details 0.35 mM 2H,15N,13C-labeled LptE

#	Name	Isotope labeling	Concentration
13	sodium phosphate	natural abundance	50 mM
14	sodium chloride	natural abundance	25 mM
15	LptE	2H,15N,13C-labeled	0.35 mM
16	H2O	natural abundance	90 %
17	D2O	natural abundance	10 %

7 3D HCCH-TOCSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5, Details 0.35 mM 15N,13C-labeled LptE

#	Name	Isotope labeling	Concentration
7	sodium phosphate	natural abundance	50 mM
8	sodium chloride	natural abundance	25 mM
9	CHAPS	natural abundance	20 mM
10	LptE	15N,13C-labeled	0.35 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

8 3D 1H-15N NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5, Details 0.35 mM 15N,13C-labeled LptE

#	Name	Isotope labeling	Concentration
7	sodium phosphate	natural abundance	50 mM
8	sodium chloride	natural abundance	25 mM
9	CHAPS	natural abundance	20 mM
10	LptE	15N,13C-labeled	0.35 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

9 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5, Details 0.35 mM 15N,13C-labeled LptE

#	Name	Isotope labeling	Concentration
7	sodium phosphate	natural abundance	50 mM
8	sodium chloride	natural abundance	25 mM
9	CHAPS	natural abundance	20 mM
10	LptE	15N,13C-labeled	0.35 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

10 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5, Details 0.35 mM 15N,13C-labeled LptE

#	Name	Isotope labeling	Concentration
7	sodium phosphate	natural abundance	50 mM
8	sodium chloride	natural abundance	25 mM
9	CHAPS	natural abundance	20 mM
10	LptE	15N,13C-labeled	0.35 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

11 3D HBHA(CO)NH

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5, Details 0.35 mM 15N,13C-labeled LptE

#	Name	Isotope labeling	Concentration
7	sodium phosphate	natural abundance	50 mM
8	sodium chloride	natural abundance	25 mM
9	CHAPS	natural abundance	20 mM
10	LptE	15N,13C-labeled	0.35 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25869_2n8x.nef
Input source #2: Coordindates	2n8x.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-------
GTSGFQLRGLGDAQFALKEIDVSARNAYGPTVRELKETLENSGVKVTSNAPYHLVLVREDNQQRTVSYTGSARGAEFELTNTINYEIVGANDLVLMSNQV
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GTSGFQLRGLGDAQFALKEIDVSARNAYGPTVRELKETLENSGVKVTSNAPYHLVLVREDNQQRTVSYTGSARGAEFELTNTINYEIVGANDLVLMSNQV
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

120-------130-------140-------150-------160-------170-------180---
QVQKVYVHDENNLIGSDQEAAQLRSEMRRDLIQQLSMRLQALTPAQLDEAQRQAEAKAKAEAEALR
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
QVQKVYVHDENNLIGSDQEAAQLRSEMRRDLIQQLSMRLQALTPAQLDEAQRQAEAKAKAEAEALR
-------110-------120-------130-------140-------150-------160------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	166	0	0	100.0

Content subtype: combined_25869_2n8x.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1461		90.4 (chain: A, length: 166)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	3069 (1)	noe	96.4 (chain: A, length: 166)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	236 (236)	.	81.9 (chain: A, length: 166)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 166, Sequence coverage: 90.4%
- Total number of assignments
  - ¹H chemical shifts: 764
  - ¹³C chemical shifts: 547
  - ¹⁵N chemical shifts: 150
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	980	763	77.9
¹³C chemical shifts	715	547	76.5
¹⁵N chemical shifts	200	150	75.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	339	303	89.4
¹³C chemical shifts	332	260	78.3
¹⁵N chemical shifts	163	143	87.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	641	460	71.8
¹³C chemical shifts	383	287	74.9
¹⁵N chemical shifts	37	7	18.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	103	93	90.3
¹³C chemical shifts	103	88	85.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	39	24	61.5
¹³C chemical shifts	39	18	46.2

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 166, Sequence coverage: 96.4%
- Total number of restraints: 3044
- Weight of restraints: 1.0 (3044)
- Potential type of restraints: upper-bound-parabolic (3044)
- Range of distance target values: 2.2, 5.5 (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

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 166, Sequence coverage: 81.9%
- Total number of restraints: 236
- Total number of restraints per polymer type: 236
- Weight of restraints: 1.0 (236)
- Potential type of restraints: square-well-parabolic (236)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords LPS biosynthesis, LptE, NMR

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Found 1 Document (0.704 seconds)

BMRB: 25869

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. LptE, : 1 : 1 : 9 entities Detail

Experiments performed 11 experiments Detail

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NMR combined restraints 4 contents Detail