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BMRB: 18679

2LXJ

Backbone 1H, 13C, and 15N Chemical Shift Assignments for cold shock protein, LmCsp with dT7

Authors

Lee, J., Jeong, K., Kim, Y.

Assembly

LmCsp dT7

Entity

1. LmCsp dT7 (polymer, Thiol state: not present), 66 monomers, 7265.816 Da Detail

MEQGTVKWFN AEKGFGFIER ENGDDVFVHF SAIQGDGFKS LDEGQAVTFD VEEGQRGPQA ANVQKA

Formula weight

7265.816 Da

Source organism

Listeria monocytogenes

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.5 %, Completeness: 83.4 %, Completeness (bb): 94.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	83.4 % (628 of 753)	83.1 % (325 of 391)	80.1 % (230 of 287)	97.3 % (73 of 75)
Backbone	94.4 % (372 of 394)	95.0 % (133 of 140)	93.1 % (176 of 189)	96.9 % (63 of 65)
Sidechain	74.8 % (311 of 416)	76.5 % (192 of 251)	70.3 % (109 of 155)	100.0 % (10 of 10)
Aromatic	9.3 % (8 of 86)	9.3 % (4 of 43)	7.1 % (3 of 42)	100.0 % (1 of 1)
Methyl	94.2 % (49 of 52)	88.5 % (23 of 26)	100.0 % (26 of 26)

1. LmCsp dT7

MEQGTVKWFN AEKGFGFIER ENGDDVFVHF SAIQGDGFKS LDEGQAVTFD VEEGQRGPQA ANVQKA

Show sample condition

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	LmCsp_dT7	[U-13C; U-15N]		0.8 mM
2	potassium phosphate	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	EDTA	natural abundance		0.1 mM
5	DSS	natural abundance		0.004 v/v
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

LACS Plot; CA

Referencing offset: -0.28 ppm, Outliers: 3 Detail

LACS Plot; CB

Referencing offset: -0.28 ppm, Outliers: 3 Detail

LACS Plot; HA

Referencing offset: 0.01 ppm, Outliers: 3 Detail

LACS Plot; CO

Referencing offset: 0.49 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2013-08-04

Citation

Structural and dynamic features of cold-shock proteins of Listeria monocytogenes, a psychrophilic bacterium
Lee, J., Jeong, K., Jin, B., Ryu, K., Kim, E., Ahn, J., Kim, Y.
Biochemistry (2013), 52, 2492-2504, PubMed 23506337 , DOI 10.1021/bi301641b , Abstract

Related entities 1. LmCsp dT7, : 1 : 2 : 215 entities Detail

Experiments performed 9 experiments Detail

1 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
1	LmCsp_dT7	[U-13C; U-15N]		0.8 mM
2	potassium phosphate	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	EDTA	natural abundance		0.1 mM
5	DSS	natural abundance		0.004 v/v
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

2 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
1	LmCsp_dT7	[U-13C; U-15N]		0.8 mM
2	potassium phosphate	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	EDTA	natural abundance		0.1 mM
5	DSS	natural abundance		0.004 v/v
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

3 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
1	LmCsp_dT7	[U-13C; U-15N]		0.8 mM
2	potassium phosphate	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	EDTA	natural abundance		0.1 mM
5	DSS	natural abundance		0.004 v/v
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

4 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
1	LmCsp_dT7	[U-13C; U-15N]		0.8 mM
2	potassium phosphate	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	EDTA	natural abundance		0.1 mM
5	DSS	natural abundance		0.004 v/v
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

5 3D HCCH-TOCSY

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	LmCsp_dT7	[U-13C; U-15N]		0.8 mM
2	potassium phosphate	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	EDTA	natural abundance		0.1 mM
5	DSS	natural abundance		0.004 v/v
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

6 3D HNHA

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	LmCsp_dT7	[U-13C; U-15N]		0.8 mM
2	potassium phosphate	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	EDTA	natural abundance		0.1 mM
5	DSS	natural abundance		0.004 v/v
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

7 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
1	LmCsp_dT7	[U-13C; U-15N]		0.8 mM
2	potassium phosphate	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	EDTA	natural abundance		0.1 mM
5	DSS	natural abundance		0.004 v/v
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

8 3D 1H-13C 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
1	LmCsp_dT7	[U-13C; U-15N]		0.8 mM
2	potassium phosphate	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	EDTA	natural abundance		0.1 mM
5	DSS	natural abundance		0.004 v/v
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

9 3D HN(CO)CA

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	LmCsp_dT7	[U-13C; U-15N]		0.8 mM
2	potassium phosphate	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	EDTA	natural abundance		0.1 mM
5	DSS	natural abundance		0.004 v/v
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_18679_2lxj.nef
Input source #2: Coordindates	2lxj.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------
MEQGTVKWFNAEKGFGFIERENGDDVFVHFSAIQGDGFKSLDEGQAVTFDVEEGQRGPQAANVQKA
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MEQGTVKWFNAEKGFGFIERENGDDVFVHFSAIQGDGFKSLDEGQAVTFDVEEGQRGPQAANVQKA

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	66	0	0	100.0

Content subtype: combined_18679_2lxj.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	640		98.5 (chain: A, length: 66)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	1168 (1)	noe	98.5 (chain: A, length: 66)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 66, Sequence coverage: 98.5%
- Total number of assignments
  - ¹H chemical shifts: 335
  - ¹³C chemical shifts: 232
  - ¹⁵N chemical shifts: 73
- 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_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 66, Sequence coverage: 98.5%
- Total number of restraints: 1151
- Weight of restraints: 1.0 (1151)
- Potential type of restraints: upper-bound-parabolic (1151)
- Range of distance target values: 2.27, 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

Keywords Nucleic acids, Protein