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BMRB: 18621

2M5W

NMR Chemical Shift Assignments of N terminal La motif domain of La protein

Authors

Bouras, G., Argyriou, A.I., Apostolidi, M., Chasapis, C.T., Stathopoulos, C., Bentrop, D., Spyroulias, G.A.

Assembly

La-type RNA-binding domain

Entity

1. La-type RNA-binding domain (polymer, Thiol state: all free), 91 monomers, 10534.79 Da Detail

MSEETSTQIL KQVEYYFSDS NFPRDKFLRS EAAKNVDNYI SIDVIASFNR MKTISTDLQL ITEALKKSTR LQVSEDGKMV RRLDPLPENI D

Formula weight

10534.79 Da

Source organism

Dictyostelium discoideum

Exptl. method

Refine. method

molecular dynamics, restrained energy minimization

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.8 %, Completeness: 82.9 %, Completeness (bb): 95.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	82.9 % (903 of 1089)	74.6 % (426 of 571)	92.2 % (388 of 421)	91.8 % (89 of 97)
Backbone	95.0 % (513 of 540)	94.4 % (170 of 180)	96.0 % (261 of 272)	93.2 % (82 of 88)
Sidechain	74.8 % (478 of 639)	65.5 % (256 of 391)	90.0 % (215 of 239)	77.8 % (7 of 9)
Aromatic	21.9 % (14 of 64)	0.0 % (0 of 32)	43.8 % (14 of 32)
Methyl	93.0 % (93 of 100)	86.0 % (43 of 50)	100.0 % (50 of 50)

1. La motif

MSEETSTQIL KQVEYYFSDS NFPRDKFLRS EAAKNVDNYI SIDVIASFNR MKTISTDLQL ITEALKKSTR LQVSEDGKMV RRLDPLPENI D

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	La-type RNA-binding domain	[U-98% 15N]		0.37 mM
2	buffer salts	natural abundance		50 mM

Sample #2

Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
3	La-type RNA-binding domain	[U-98% 13C; U-98% 15N]		0.37 mM
4	buffer salts	natural abundance		50 mM

LACS Plot; CA

Referencing offset: -1.04 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: -1.04 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: 0.07 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 0.09 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 31 models in PDB: 2M5W, Strand ID: A Detail

Release date

2012-07-26

Citation

¹H, ¹⁵N, ¹³C assignment and secondary structure determination of two domains of La protein from D. discoideum
Apostolidi, M., Vourtsis, D.J., Chasapis, C.T., Stathopoulos, C., Bentrop, D., Spyroulias, G.A.
Biomol. NMR Assign. (2014), 8, 47-51, PubMed 23239108 , DOI 10.1007/s12104-012-9450-6 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 18620 released on 2012-07-26
Title NMR Chemical Shift Assignments of N terminal RRM domain of La protein

Related entities 1. La-type RNA-binding domain, : 1 : 1 : 138 entities Detail

Experiments performed 8 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 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	La-type RNA-binding domain	[U-98% 15N]		0.37 mM
2	buffer salts	natural abundance		50 mM

2 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
3	La-type RNA-binding domain	[U-98% 13C; U-98% 15N]		0.37 mM
4	buffer salts	natural abundance		50 mM

3 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
3	La-type RNA-binding domain	[U-98% 13C; U-98% 15N]		0.37 mM
4	buffer salts	natural abundance		50 mM

4 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
3	La-type RNA-binding domain	[U-98% 13C; U-98% 15N]		0.37 mM
4	buffer salts	natural abundance		50 mM

5 3D HNCA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
3	La-type RNA-binding domain	[U-98% 13C; U-98% 15N]		0.37 mM
4	buffer salts	natural abundance		50 mM

6 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
3	La-type RNA-binding domain	[U-98% 13C; U-98% 15N]		0.37 mM
4	buffer salts	natural abundance		50 mM

7 3D HN(CO)CA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
3	La-type RNA-binding domain	[U-98% 13C; U-98% 15N]		0.37 mM
4	buffer salts	natural abundance		50 mM

8 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 7

#	Name	Isotope labeling	Type	Concentration
3	La-type RNA-binding domain	[U-98% 13C; U-98% 15N]		0.37 mM
4	buffer salts	natural abundance		50 mM

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_18621_2m5w.nef
Input source #2: Coordindates	2m5w.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--------70--------80--------90-
MSEETSTQILKQVEYYFSDSNFPRDKFLRSEAAKNVDNYISIDVIASFNRMKTISTDLQLITEALKKSTRLQVSEDGKMVRRLDPLPENID
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MSEETSTQILKQVEYYFSDSNFPRDKFLRSEAAKNVDNYISIDVIASFNRMKTISTDLQLITEALKKSTRLQVSEDGKMVRRLDPLPENID

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	91	0	0	100.0

Content subtype: combined_18621_2m5w.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	909		96.7 (chain: A, length: 91)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	1414 (1)	noe	97.8 (chain: A, length: 91)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 91, Sequence coverage: 96.7%
- Total number of assignments
  - ¹H chemical shifts: 468
  - ¹³C chemical shifts: 361
  - ¹⁵N chemical shifts: 80
- 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: 91, Sequence coverage: 97.8%
- Total number of restraints: 1414
- Weight of restraints: 1.0 (1414)
- Potential type of restraints: upper-bound-parabolic (1414)
- Range of distance target values: 2.6, 10.04 (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