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BMRB: 18118

2LMI

NMR structure of the protein BC040485 from Homo sapiens

Authors

Dutta, S.K., Serrano, P., Geralt, M., Wuthrich, K., JCSG, J.

Assembly

BC040485

Entity

1. BC040485 (polymer, Thiol state: all free), 107 monomers, 12426.88 Da Detail

GSKLEEEVDD VFLIRAQGLP WSCTMEDVLN FFSDCRIRNG ENGIHFLLNR DGKRRGDALI EMESEQDVQK ALEKHRMYMG QRYVEVYEIN NEDVDALMKS LQVKSSP

Formula weight

12426.88 Da

Source organism

Exptl. method

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.2 %, Completeness: 83.1 %, Completeness (bb): 81.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	83.1 % (1051 of 1264)	88.0 % (585 of 665)	72.8 % (351 of 482)	98.3 % (115 of 117)
Backbone	81.3 % (519 of 638)	93.2 % (204 of 219)	67.5 % (212 of 314)	98.1 % (103 of 105)
Sidechain	86.5 % (628 of 726)	85.4 % (381 of 446)	87.7 % (235 of 268)	100.0 % (12 of 12)
Aromatic	65.5 % (55 of 84)	64.3 % (27 of 42)	65.9 % (27 of 41)	100.0 % (1 of 1)
Methyl	93.1 % (95 of 102)	92.2 % (47 of 51)	94.1 % (48 of 51)

1. entity

GSKLEEEVDD VFLIRAQGLP WSCTMEDVLN FFSDCRIRNG ENGIHFLLNR DGKRRGDALI EMESEQDVQK ALEKHRMYMG QRYVEVYEIN NEDVDALMKS LQVKSSP

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium azide	natural abundance		5 mM
4	sodium chloride	natural abundance		50 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

LACS Plot; CA

Referencing offset: 2.71 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: 2.71 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.05 ppm, Outliers: 2 Detail

Protein Blocks Logo

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

Release date

2012-01-24

Citation

NMR structure of the human RNA binding protein BC040485
Dutta, S.K., Serrano, P., Geralt, M., Wuthrich, K.
Not known

Related entities 1. BC040485, : 1 : 1 : 2 : 146 entities Detail

Interaction partners 1. BC040485, : 12 interactors Detail

More details for 12 interactors identified by 7 citations

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium azide	natural abundance		5 mM
4	sodium chloride	natural abundance		50 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

2 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium azide	natural abundance		5 mM
4	sodium chloride	natural abundance		50 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

3 3D HNCA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium azide	natural abundance		5 mM
4	sodium chloride	natural abundance		50 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

4 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium azide	natural abundance		5 mM
4	sodium chloride	natural abundance		50 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

5 4D HACANH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium azide	natural abundance		5 mM
4	sodium chloride	natural abundance		50 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

6 5D HACACONH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium azide	natural abundance		5 mM
4	sodium chloride	natural abundance		50 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

7 5D CBCACONH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium azide	natural abundance		5 mM
4	sodium chloride	natural abundance		50 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

8 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium azide	natural abundance		5 mM
4	sodium chloride	natural abundance		50 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

9 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium azide	natural abundance		5 mM
4	sodium chloride	natural abundance		50 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

10 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium azide	natural abundance		5 mM
4	sodium chloride	natural abundance		50 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_18118_2lmi.nef
Input source #2: Coordindates	2lmi.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
GSKLEEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALEKHRMYMGQRYVEVYEINNEDVDALMKS
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSKLEEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALEKHRMYMGQRYVEVYEINNEDVDALMKS

-------
LQVKSSP
|||||||
LQVKSSP

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	107	0	0	100.0

Content subtype: combined_18118_2lmi.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1043		95.3 (chain: A, length: 107)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	1939 (1)	noe	95.3 (chain: A, length: 107)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 107, Sequence coverage: 95.3%
- Total number of assignments
  - ¹H chemical shifts: 590
  - ¹³C chemical shifts: 340
  - ¹⁵N chemical shifts: 113
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 107, Sequence coverage: 95.3%
- Total number of restraints: 1939
- Weight of restraints: 1.0 (1939)
- Potential type of restraints: upper-bound-parabolic (1939)
- Range of distance target values: 2.4, 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 RNA binding, RRM, Homo sapiens G-rich RNA sequence binding factor, RNA binding domain