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Found 1 Document (0.883 seconds)

BMRB: 18535

2LUQ

SOLUTION STRUCTURE OF DOUBLE-STRANDED RNA BINDING DOMAIN OF S.CEREVISIAE RNASE III (RNT1P)

Authors

Wang, Z., Feigon, J.

Assembly

Ribonuclease III

Entity

1. Ribonuclease III (polymer, Thiol state: all free), 90 monomers, 9806.233 Da Detail

GSLDMNAKRQ LYSLIGYASL RLHYVTVKKP TAVDPNSIVE CRVGDGTVLG TGVGRNIKIA GIRAAENALR DKKMLDFYAK QRAAIPRSES

Formula weight

9806.233 Da

Source organism

Saccharomyces cerevisiae

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.9 %, Completeness: 87.5 %, Completeness (bb): 96.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	87.5 % (895 of 1023)	85.0 % (453 of 533)	89.9 % (357 of 397)	91.4 % (85 of 93)
Backbone	96.4 % (515 of 534)	95.1 % (176 of 185)	97.3 % (255 of 262)	96.6 % (84 of 87)
Sidechain	80.2 % (458 of 571)	79.0 % (275 of 348)	83.9 % (182 of 217)	16.7 % (1 of 6)
Aromatic	34.8 % (16 of 46)	69.6 % (16 of 23)	0.0 % (0 of 23)
Methyl	95.5 % (107 of 112)	94.6 % (53 of 56)	96.4 % (54 of 56)

1. Ribonuclease III

GSLDMNAKRQ LYSLIGYASL RLHYVTVKKP TAVDPNSIVE CRVGDGTVLG TGVGRNIKIA GIRAAENALR DKKMLDFYAK QRAAIPRSES

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 20 mM phosphate, Ph6.5, 150mM NaCl

#	Name	Isotope labeling	Concentration
1	Ribonuclease III	[U-100% 13C; U-100% 15N]	1 mM
2	H2O	natural abundance	90 %
3	D2O	[U-100% 2H]	10 %
4	sodium chloride	natural abundance	150 mM
5	sodium phosphate	natural abundance	20 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 20 mM phosphate, Ph6.5, 150mM NaCl

#	Name	Isotope labeling	Concentration
6	Ribonuclease III	[U-100% 13C; U-100% 15N]	1 mM
7	D2O	[U-100% 2H]	100 %
8	sodium chloride	natural abundance	150 mM
9	sodium phosphate	natural abundance	20 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.19 ppm, Outliers: 3 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.19 ppm, Outliers: 3 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.05 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.03 ppm, Outliers: 2 Detail

Protein Blocks Logo

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

Release date

2012-08-28

Citation

Structure of a yeast RNase III dsRBD complex with a noncanonical RNA substrate provides new insights into binding specificity of dsRBDs
Wang, Z., Hartman, E., Roy, K., Chanfreau, G., Feigon, J.
Structure (2011), 19, 999-1010, PubMed 21742266 , DOI 10.1016/j.str.2011.03.022 , Abstract

Related entities 1. Ribonuclease III, : 1 : 3 : 6 : 1 entities Detail

Interaction partners 1. Ribonuclease III, : 26 interactors Detail

More details for 26 interactors identified by 10 citations

Experiments performed 8 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 20 mM phosphate, Ph6.5, 150mM NaCl

#	Name	Isotope labeling	Concentration
1	Ribonuclease III	[U-100% 13C; U-100% 15N]	1 mM
2	H2O	natural abundance	90 %
3	D2O	[U-100% 2H]	10 %
4	sodium chloride	natural abundance	150 mM
5	sodium phosphate	natural abundance	20 mM

2 3D HNCACB

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 20 mM phosphate, Ph6.5, 150mM NaCl

#	Name	Isotope labeling	Concentration
1	Ribonuclease III	[U-100% 13C; U-100% 15N]	1 mM
2	H2O	natural abundance	90 %
3	D2O	[U-100% 2H]	10 %
4	sodium chloride	natural abundance	150 mM
5	sodium phosphate	natural abundance	20 mM

3 3D CBCA(CO)NH

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 20 mM phosphate, Ph6.5, 150mM NaCl

#	Name	Isotope labeling	Concentration
1	Ribonuclease III	[U-100% 13C; U-100% 15N]	1 mM
2	H2O	natural abundance	90 %
3	D2O	[U-100% 2H]	10 %
4	sodium chloride	natural abundance	150 mM
5	sodium phosphate	natural abundance	20 mM

4 3D HNCO

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 20 mM phosphate, Ph6.5, 150mM NaCl

#	Name	Isotope labeling	Concentration
1	Ribonuclease III	[U-100% 13C; U-100% 15N]	1 mM
2	H2O	natural abundance	90 %
3	D2O	[U-100% 2H]	10 %
4	sodium chloride	natural abundance	150 mM
5	sodium phosphate	natural abundance	20 mM

5 3D HCCH-TOCSY

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 20 mM phosphate, Ph6.5, 150mM NaCl

#	Name	Isotope labeling	Concentration
6	Ribonuclease III	[U-100% 13C; U-100% 15N]	1 mM
7	D2O	[U-100% 2H]	100 %
8	sodium chloride	natural abundance	150 mM
9	sodium phosphate	natural abundance	20 mM

6 3D HCCH-COSY

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 20 mM phosphate, Ph6.5, 150mM NaCl

#	Name	Isotope labeling	Concentration
6	Ribonuclease III	[U-100% 13C; U-100% 15N]	1 mM
7	D2O	[U-100% 2H]	100 %
8	sodium chloride	natural abundance	150 mM
9	sodium phosphate	natural abundance	20 mM

7 3D 1H-15N NOESY

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 20 mM phosphate, Ph6.5, 150mM NaCl

#	Name	Isotope labeling	Concentration
1	Ribonuclease III	[U-100% 13C; U-100% 15N]	1 mM
2	H2O	natural abundance	90 %
3	D2O	[U-100% 2H]	10 %
4	sodium chloride	natural abundance	150 mM
5	sodium phosphate	natural abundance	20 mM

8 3D 1H-13C NOESY aliphatic

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 20 mM phosphate, Ph6.5, 150mM NaCl

#	Name	Isotope labeling	Concentration
6	Ribonuclease III	[U-100% 13C; U-100% 15N]	1 mM
7	D2O	[U-100% 2H]	100 %
8	sodium chloride	natural abundance	150 mM
9	sodium phosphate	natural abundance	20 mM

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_18535_2luq.nef
Input source #2: Coordindates	2luq.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

----370-------380-------390-------400-------410-------420-------430-------440-------450---
GSLDMNAKRQLYSLIGYASLRLHYVTVKKPTAVDPNSIVECRVGDGTVLGTGVGRNIKIAGIRAAENALRDKKMLDFYAKQRAAIPRSES
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSLDMNAKRQLYSLIGYASLRLHYVTVKKPTAVDPNSIVECRVGDGTVLGTGVGRNIKIAGIRAAENALRDKKMLDFYAKQRAAIPRSES
--------10--------20--------30--------40--------50--------60--------70--------80--------90

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	90	0	0	100.0

Content subtype: combined_18535_2luq.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	872		98.9 (chain: A, length: 90)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	1899 (1)	noe	92.2 (chain: A, length: 90)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	62 (1)	hbond	48.9 (chain: A, length: 90)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	145 (145)	.	91.1 (chain: A, length: 90)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_5	OK	55 (55)	.	61.1 (chain: A, length: 90)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 90, Sequence coverage: 98.9%
- Total number of assignments
  - ¹³C chemical shifts: 355
  - ¹H chemical shifts: 433
  - ¹⁵N chemical shifts: 84
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
386	HIS	HD1	6.74

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	397	355	89.4
¹H chemical shifts	533	432	81.1
¹⁵N chemical shifts	101	84	83.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	180	173	96.1
¹H chemical shifts	185	174	94.1
¹⁵N chemical shifts	87	84	96.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	217	182	83.9
¹H chemical shifts	348	258	74.1
¹⁵N chemical shifts	14	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	58	55	94.8
¹H chemical shifts	58	53	91.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	23	0	0.0
¹H chemical shifts	23	16	69.6

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 90, Sequence coverage: 92.2%
- Total number of restraints: 1899
- Weight of restraints: 1.0 (1899)
- Potential type of restraints: square-well-parabolic (1899)
- Range of distance target values: 2.65, 4.15 (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
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 90, Sequence coverage: 48.9%
  - Total number of restraints: 62
  - Weight of restraints: 1.0 (62)
  - Potential type of restraints: square-well-parabolic (62)
  - Range of distance target values: 1.95, 2.95 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 90, Sequence coverage: 91.1%
- Total number of restraints: 145
- Total number of restraints per polymer type: 145
- Weight of restraints: 1.0 (145)
- Potential type of restraints: square-well-parabolic (145)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_5
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 90, Sequence coverage: 61.1%
- Total number of restraints: 55
- Potential type of restraints: square-well-parabolic (55)
- Range of observed RDC values: -17.95, 9.87 (Hz)
- Histogram of observed RDC values
- RDC restraints per residue
  - Chain_ID: A
    None

Keywords DSRBD, RNT1P

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Found 1 Document (0.883 seconds)

BMRB: 18535

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Ribonuclease III, : 1 : 3 : 6 : 1 entities Detail

Interaction partners 1. Ribonuclease III, : 26 interactors Detail

Experiments performed 8 experiments Detail

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NMR combined restraints 6 contents Detail