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BMRB: 15487

2JVR

Segmental Isotope Labeling of Npl3p

Authors

Skrisovska, L., Allain, F.H-T.

Assembly

Npl3p RRM2

Entity

1. Npl3p RRM2 (polymer, Thiol state: all free), 111 monomers, 12576.88 Da Detail

MGSSHHHHHH SSGLVPRGSH MSKLPAKRYR ITMKNLPEGC SWQDLKDLAR ENSLETTFSS VNTRDFDGTG ALEFPSEEIL VEALERLNNI EFRGSVITVE RDDNPPPIRR S

Formula weight

12576.88 Da

Source organism

Saccharomyces cerevisiae

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 73.0 %, Completeness: 61.8 %, Completeness (bb): 60.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	61.8 % (786 of 1272)	66.0 % (440 of 667)	53.1 % (262 of 493)	75.0 % (84 of 112)
Backbone	60.6 % (395 of 652)	69.8 % (155 of 222)	50.0 % (163 of 326)	74.0 % (77 of 104)
Sidechain	64.2 % (465 of 724)	64.0 % (285 of 445)	63.8 % (173 of 271)	87.5 % (7 of 8)
Aromatic	43.2 % (38 of 88)	52.3 % (23 of 44)	32.6 % (14 of 43)	100.0 % (1 of 1)
Methyl	80.0 % (80 of 100)	80.0 % (40 of 50)	80.0 % (40 of 50)

1. Npl3p RRM2

MGSSHHHHHH SSGLVPRGSH MSKLPAKRYR ITMKNLPEGC SWQDLKDLAR ENSLETTFSS VNTRDFDGTG ALEFPSEEIL VEALERLNNI EFRGSVITVE RDDNPPPIRR S

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	Npl3p RRM2	[U-13C; U-15N]		1 mM
2	H2O			90 %
3	D2O			10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Type	Concentration
4	Npl3p RRM2	[U-13C; U-15N]		1 mM
5	D2O			10 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Type	Concentration
6	Npl3p RRM2	[U-15N]		1 mM
7	H2O			90 %
8	D2O			10 %

LACS Plot; CA

Referencing offset: 2.57 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: 2.57 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.02 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2008-06-25

Citation

Improved segmental isotope labeling methods for the NMR study of multidomain or large proteins: application to the RRMs of Npl3p and hnRNP L
Skrisovska, L., Allain, F.H-T.
J. Mol. Biol. (2008), 375, 151-164, PubMed 17936301 , DOI 10.1016/j.jmb.2007.09.030 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 15485 released on 2008-06-25
Title Segmental isotope labeling of Npl3

Related entities 1. Npl3p RRM2, : 1 : 4 : 28 entities Detail

Interaction partners 1. Npl3p RRM2, : 70 interactors Detail

More details for 70 interactors identified by 16 citations

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker DRX - 500 MHz equipped with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	Npl3p RRM2	[U-13C; U-15N]		1 mM
2	H2O			90 %
3	D2O			10 %

2 2D 1H-13C HSQC

Instrument

Bruker DRX - 500 MHz equipped with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	Npl3p RRM2	[U-13C; U-15N]		1 mM
2	H2O			90 %
3	D2O			10 %

3 3D HNCA

Instrument

Bruker DRX - 500 MHz equipped with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	Npl3p RRM2	[U-13C; U-15N]		1 mM
2	H2O			90 %
3	D2O			10 %

4 3D HN(CO)CA

Instrument

Bruker DRX - 500 MHz equipped with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	Npl3p RRM2	[U-13C; U-15N]		1 mM
2	H2O			90 %
3	D2O			10 %

5 3D CBCA(CO)NH

Instrument

Bruker DRX - 500 MHz equipped with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	Npl3p RRM2	[U-13C; U-15N]		1 mM
2	H2O			90 %
3	D2O			10 %

6 3D HNCACB

Instrument

Bruker DRX - 500 MHz equipped with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	Npl3p RRM2	[U-13C; U-15N]		1 mM
2	H2O			90 %
3	D2O			10 %

7 3D 1H-15N NOESY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	Npl3p RRM2	[U-13C; U-15N]		1 mM
2	H2O			90 %
3	D2O			10 %

8 3D 1H-13C NOESY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	Npl3p RRM2	[U-13C; U-15N]		1 mM
2	H2O			90 %
3	D2O			10 %

9 3D HCCH-TOCSY

Instrument

Bruker DRX - 500 MHz equipped with cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Type	Concentration
1	Npl3p RRM2	[U-13C; U-15N]		1 mM
2	H2O			90 %
3	D2O			10 %

10 2D 1H-1H TOCSY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Type	Concentration
4	Npl3p RRM2	[U-13C; U-15N]		1 mM
5	D2O			10 %

11 2D 1H-1H NOESY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 7

#	Name	Isotope labeling	Type	Concentration
4	Npl3p RRM2	[U-13C; U-15N]		1 mM
5	D2O			10 %

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15487_2jvr.nef
Input source #2: Coordindates	2jvr.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-------100
MGSSHHHHHHSSGLVPRGSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGSSHHHHHHSSGLVPRGSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVE

-------110-
RDDNPPPIRRS
|||||||||||
RDDNPPPIRRS

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	111	0	0	100.0

Content subtype: combined_15487_2jvr.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	735		70.3 (chain: A, length: 111)
1	Distance restraints	AMBER_distance_constraints_2	OK	1995 (1)	noe	69.4 (chain: A, length: 111)
2	Distance restraints	AMBER_distance_constraints_4	Warning	32 (1)	noe	23.4 (chain: A, length: 111)
3	Distance restraints	AMBER_distance_constraints_3	OK	58 (1)	hbond	34.2 (chain: A, length: 111)
1	Dihedral angle restraints	AMBER_dihedral_6	Warning	1 (1)	.	1.8 (chain: A, length: 111)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 111, Sequence coverage: 70.3%
- Total number of assignments
  - ¹H chemical shifts: 423
  - ¹³C chemical shifts: 230
  - ¹⁵N chemical shifts: 82
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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: AMBER_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 111, Sequence coverage: 69.4%
- Total number of restraints: 1995
- Weight of restraints: 1.0 (1995)
- Potential type of restraints: square-well-parabolic (1995)
- Range of distance target values: 2.54, 5.12 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: AMBER_distance_constraints_4
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 111, Sequence coverage: 23.4%
  - Total number of restraints: 32
  - Weight of restraints: 1.0 (32)
  - Potential type of restraints: square-well-parabolic (32)
  - Range of distance target values: 3.9, 4.24 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map
  - Saveframe: AMBER_distance_constraints_3
    - Status: OK
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 111, Sequence coverage: 34.2%
    - Total number of restraints: 58
    - Weight of restraints: 1.0 (58)
    - Potential type of restraints: square-well-parabolic (58)
    - Range of distance target values: 2.15, 2.65 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
    - Distance restraints on contact map

Dihedral angle restraints

Saveframe: AMBER_dihedral_6
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 111, Sequence coverage: 1.8%
- Total number of restraints: 1
- Total number of restraints per polymer type: 1
- Weight of restraints: 1.0 (1)
- Potential type of restraints: square-well-parabolic (1)
- Dihedral angle restraints per residue

Keywords EPL, NMR, Segmental labeling, Structural Biology