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BMRB: 16256

2KHX

Drosha RNA Binding Domain

Authors

Mueller, G.A., Miller, M., Ghosh, M., DeRose, E.F., London, R.E., Hall, T.

Assembly

Drosha

Entity

1. Drosha (polymer, Thiol state: unknown), 90 monomers, 10055.35 Da Detail

GSPQFMLNQD WNDPKSQLQQ CCLTLRTEGK EPDIPLYKTL QTVGPSHART YTVAVYFKGE RIGCGKGPSI QQAEMGAAMD ALEKYNFPQM

Formula weight

10055.35 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 81.1 %, Completeness: 68.2 %, Completeness (bb): 64.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	68.2 % (717 of 1052)	72.2 % (400 of 554)	61.7 % (248 of 402)	71.9 % (69 of 96)
Backbone	64.3 % (338 of 526)	73.5 % (133 of 181)	53.8 % (141 of 262)	77.1 % (64 of 83)
Sidechain	73.2 % (445 of 608)	71.6 % (267 of 373)	77.9 % (173 of 222)	38.5 % (5 of 13)
Aromatic	66.7 % (52 of 78)	66.7 % (26 of 39)	68.4 % (26 of 38)	0.0 % (0 of 1)
Methyl	94.7 % (72 of 76)	94.7 % (36 of 38)	94.7 % (36 of 38)

1. binding domain

GSPQFMLNQD WNDPKSQLQQ CCLTLRTEGK EPDIPLYKTL QTVGPSHART YTVAVYFKGE RIGCGKGPSI QQAEMGAAMD ALEKYNFPQM

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1.0 ~ 2.0 mM
2	TRIS	[U-2H]		25 mM
3	potassium chloride	natural abundance		100 mM
4	DTT	[U-2H]		1 mM
5	EDTA	natural abundance		1 mM
6	DSS	natural abundance		10 uM

LACS Plot; CA

Referencing offset: -0.45 ppm, Outliers: 3 Detail

LACS Plot; CB

Referencing offset: -0.45 ppm, Outliers: 3 Detail

LACS Plot; HA

Referencing offset: -0.04 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2KHX, Strand ID: A Detail

Release date

2010-03-31

Citation

Solution structure of the Drosha double-stranded RNA-binding domain
Mueller, G., Miller, M., DeRose, E., Ghosh, M., London, R., Hall, T.
Silence (2010), 1, 2-2, PubMed 20226070 , DOI 10.1186/1758-907X-1-2 , Abstract

Related entities 1. Drosha, : 1 : 92 entities Detail

Interaction partners 1. Drosha, : 29 interactors Detail

More details for 29 interactors identified by 15 citations

Experiments performed 9 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1.0 ~ 2.0 mM
2	TRIS	[U-2H]		25 mM
3	potassium chloride	natural abundance		100 mM
4	DTT	[U-2H]		1 mM
5	EDTA	natural abundance		1 mM
6	DSS	natural abundance		10 uM

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1.0 ~ 2.0 mM
2	TRIS	[U-2H]		25 mM
3	potassium chloride	natural abundance		100 mM
4	DTT	[U-2H]		1 mM
5	EDTA	natural abundance		1 mM
6	DSS	natural abundance		10 uM

3 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1.0 ~ 2.0 mM
2	TRIS	[U-2H]		25 mM
3	potassium chloride	natural abundance		100 mM
4	DTT	[U-2H]		1 mM
5	EDTA	natural abundance		1 mM
6	DSS	natural abundance		10 uM

4 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1.0 ~ 2.0 mM
2	TRIS	[U-2H]		25 mM
3	potassium chloride	natural abundance		100 mM
4	DTT	[U-2H]		1 mM
5	EDTA	natural abundance		1 mM
6	DSS	natural abundance		10 uM

5 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1.0 ~ 2.0 mM
2	TRIS	[U-2H]		25 mM
3	potassium chloride	natural abundance		100 mM
4	DTT	[U-2H]		1 mM
5	EDTA	natural abundance		1 mM
6	DSS	natural abundance		10 uM

6 3D H(CCO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1.0 ~ 2.0 mM
2	TRIS	[U-2H]		25 mM
3	potassium chloride	natural abundance		100 mM
4	DTT	[U-2H]		1 mM
5	EDTA	natural abundance		1 mM
6	DSS	natural abundance		10 uM

7 3D C(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1.0 ~ 2.0 mM
2	TRIS	[U-2H]		25 mM
3	potassium chloride	natural abundance		100 mM
4	DTT	[U-2H]		1 mM
5	EDTA	natural abundance		1 mM
6	DSS	natural abundance		10 uM

8 CN-4D simultaneous NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1.0 ~ 2.0 mM
2	TRIS	[U-2H]		25 mM
3	potassium chloride	natural abundance		100 mM
4	DTT	[U-2H]		1 mM
5	EDTA	natural abundance		1 mM
6	DSS	natural abundance		10 uM

9 HB-HE/HD-aromatic

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1.0 ~ 2.0 mM
2	TRIS	[U-2H]		25 mM
3	potassium chloride	natural abundance		100 mM
4	DTT	[U-2H]		1 mM
5	EDTA	natural abundance		1 mM
6	DSS	natural abundance		10 uM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_16256_2khx.nef
Input source #2: Coordindates	2khx.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

-1260---1270------1280------1290------1300------1310------1320------1330------1340---
NDPKSQLQQCCLTLRTEGKEPDIPLYKTLQTVGPSHARTYTVAVYFKGERIGCGKGPSIQQAEMGAAMDALEKYNFPQMHHHHHH
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
NDPKSQLQQCCLTLRTEGKEPDIPLYKTLQTVGPSHARTYTVAVYFKGERIGCGKGPSIQQAEMGAAMDALEKYNFPQMHHHHHH
--------10--------20--------30--------40--------50--------60--------70--------80-----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	85	0	0	100.0

Content subtype: combined_16256_2khx.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	712		84.7 (chain: A, length: 85)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	777 (1)	noe	80.0 (chain: A, length: 85)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	189 (189)	.	89.4 (chain: A, length: 85)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 85, Sequence coverage: 84.7%
- Total number of assignments
  - ¹H chemical shifts: 399
  - ¹³C chemical shifts: 245
  - ¹⁵N chemical shifts: 68
- 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: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 85, Sequence coverage: 80.0%
- Total number of restraints: 767
- Weight of restraints: 1.0 (767)
- Potential type of restraints: square-well-parabolic (767)
- Range of distance target values: 2.25, 3.9 (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

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 85, Sequence coverage: 89.4%
- Total number of restraints: 189
- Total number of restraints per polymer type: 189
- Weight of restraints: 1.0 (189)
- Potential type of restraints: square-well-parabolic (189)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A