BMRBj - BMREntryMaster

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BMRB: 19792

2MKS

NMR structure of the RRM domain of RBMX from homo sapiens

Authors

Serrano, P., Geralt, M., Wuthrich, K.

Assembly

RBMX

Entity

1. RBMX (polymer, Thiol state: not present), 92 monomers, 10077.31 Da Detail

GHMVEADRPG KLFIGGLNTE TNEKALEAVF GKYGRIVEVL LMKDRETNKS RGFAFVTFES PADAKDAARD MNGKSLDGKA IKVEQATKPS FE

Formula weight

10077.31 Da

Source organism

Exptl. method

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 91.7 %, Completeness (bb): 98.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	91.7 % (967 of 1054)	90.4 % (498 of 551)	91.9 % (376 of 409)	98.9 % (93 of 94)
Backbone	98.4 % (537 of 546)	97.9 % (186 of 190)	98.5 % (263 of 267)	98.9 % (88 of 89)
Sidechain	86.6 % (512 of 591)	86.4 % (312 of 361)	86.7 % (195 of 225)	100.0 % (5 of 5)
Aromatic	73.6 % (53 of 72)	83.3 % (30 of 36)	63.9 % (23 of 36)
Methyl	100.0 % (90 of 90)	100.0 % (45 of 45)	100.0 % (45 of 45)

1. entity

GHMVEADRPG KLFIGGLNTE TNEKALEAVF GKYGRIVEVL LMKDRETNKS RGFAFVTFES PADAKDAARD MNGKSLDGKA IKVEQATKPS FE

Show sample condition

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium chloride	natural abundance		100 mM
3	sodium acetate	[U-99% 2H]		10 mM
4	sodium azide	natural abundance		5 mM
5	DTT	natural abundance		2 mM

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: 0.1 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 2.7 ppm, Outliers: 2 Detail

Protein Blocks Logo

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

Release date

2014-03-09

Citation

NMR structure of the first RRM domain of the protein RBM39 from homo sapiens
Serrano, P., Wuthrich, K., Geralt, M., Dutta, S.K.
Not known

Related entities 1. RBMX, : 1 : 8 : 337 entities Detail

Interaction partners 1. RBMX, : 37 interactors Detail

More details for 37 interactors identified by 6 citations

Experiments performed 7 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 5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium chloride	natural abundance		100 mM
3	sodium acetate	[U-99% 2H]		10 mM
4	sodium azide	natural abundance		5 mM
5	DTT	natural abundance		2 mM

2 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 600 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium chloride	natural abundance		100 mM
3	sodium acetate	[U-99% 2H]		10 mM
4	sodium azide	natural abundance		5 mM
5	DTT	natural abundance		2 mM

3 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 600 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium chloride	natural abundance		100 mM
3	sodium acetate	[U-99% 2H]		10 mM
4	sodium azide	natural abundance		5 mM
5	DTT	natural abundance		2 mM

4 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium chloride	natural abundance		100 mM
3	sodium acetate	[U-99% 2H]		10 mM
4	sodium azide	natural abundance		5 mM
5	DTT	natural abundance		2 mM

5 4D APSY HACANH

Instrument

Bruker Avance - 600 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium chloride	natural abundance		100 mM
3	sodium acetate	[U-99% 2H]		10 mM
4	sodium azide	natural abundance		5 mM
5	DTT	natural abundance		2 mM

6 5D APSY CBCACONH

Instrument

Bruker Avance - 600 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium chloride	natural abundance		100 mM
3	sodium acetate	[U-99% 2H]		10 mM
4	sodium azide	natural abundance		5 mM
5	DTT	natural abundance		2 mM

7 5D APSY HACACONH

Instrument

Bruker Avance - 600 MHz

Sample

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

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium chloride	natural abundance		100 mM
3	sodium acetate	[U-99% 2H]		10 mM
4	sodium azide	natural abundance		5 mM
5	DTT	natural abundance		2 mM

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_19792_2mks.nef
Input source #2: Coordindates	2mks.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--
GHMVEADRPGKLFIGGLNTETNEKALEAVFGKYGRIVEVLLMKDRETNKSRGFAFVTFESPADAKDAARDMNGKSLDGKAIKVEQATKPSFE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GHMVEADRPGKLFIGGLNTETNEKALEAVFGKYGRIVEVLLMKDRETNKSRGFAFVTFESPADAKDAARDMNGKSLDGKAIKVEQATKPSFE

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	92	0	0	100.0

Content subtype: combined_19792_2mks.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	949		98.9 (chain: A, length: 92)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	705 (1)	noe	90.2 (chain: A, length: 92)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 92, Sequence coverage: 98.9%
- Total number of assignments
  - ¹H chemical shifts: 491
  - ¹³C chemical shifts: 366
  - ¹⁵N chemical shifts: 92
- 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

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 92, Sequence coverage: 90.2%
- Total number of restraints: 704
- Weight of restraints: 1.0 (704)
- Potential type of restraints: upper-bound-parabolic (704)
- 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 PSI:Biology, RBMX, RNA binding protein, RRM, T-Cell