BMRBj - BMREntryMaster

Found 1 Document (0.851 seconds)

BMRB: 25138

2N3F

Chemical shift assignments of DRB4(1-153), a dsRNA binding protein in A. thaliana RNAi pathway

Authors

Deshmukh, M., Chiliveri, S.

Assembly

DRB4(1-153)

Entity

1. DRB4(1-153) (polymer, Thiol state: all free), 153 monomers, 16599.55 Da Detail

MDHVYKGQLQ AYALQHNLEL PVYANEREGP PHAPRFRCNV TFCGQTFQSS EFFPTLKSAE HAAAKIAVAS LTPQSPEGID VAYKNLLQEI AQKESSLLPF YATATSGPSH APTFTSTVEF AGKVFSGEEA KTKKLAEMSA AKVAFMSIKN GNS

Formula weight

16599.55 Da

Source organism

Arabidopsis thaliana

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.3 %, Completeness: 87.7 %, Completeness (bb): 97.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	87.7 % (1533 of 1748)	89.2 % (806 of 904)	83.8 % (576 of 687)	96.2 % (151 of 157)
Backbone	97.8 % (878 of 898)	97.0 % (295 of 304)	98.0 % (442 of 451)	98.6 % (141 of 143)
Sidechain	80.0 % (796 of 995)	85.2 % (511 of 600)	72.2 % (275 of 381)	71.4 % (10 of 14)
Aromatic	35.6 % (57 of 160)	66.3 % (53 of 80)	5.0 % (4 of 80)
Methyl	95.5 % (147 of 154)	97.4 % (75 of 77)	93.5 % (72 of 77)

1. DRB4(1-153)

MDHVYKGQLQ AYALQHNLEL PVYANEREGP PHAPRFRCNV TFCGQTFQSS EFFPTLKSAE HAAAKIAVAS LTPQSPEGID VAYKNLLQEI AQKESSLLPF YATATSGPSH APTFTSTVEF AGKVFSGEEA KTKKLAEMSA AKVAFMSIKN GNS

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
1	DRB4(1-153)	[U-100% 15N]	0.5 mM
2	Potassium phosphate buffer	natural abundance	50 mM
3	Na2SO4	natural abundance	100 mM
4	DTT	natural abundance	4 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
5	DRB4(1-153)	[U-100% 13C; U-100% 15N]	0.5 mM
6	Potassium phosphate buffer	natural abundance	50 mM
7	Na2SO4	natural abundance	100 mM
8	DTT	natural abundance	4 mM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
9	DRB4(1-153)	[U-10% 13C; U-100% 15N]	0.5 mM
10	Potassium phosphate buffer	natural abundance	50 mM
11	Na2SO4	natural abundance	100 mM
12	DTT	natural abundance	4 mM

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
13	DRB4(1-153)	[U-100% 15N]	0.5 mM
14	Potassium phosphate buffer	natural abundance	50 mM
15	Na2SO4	natural abundance	100 mM
16	DTT	natural abundance	4 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	0.0 ppm	na	indirect	0.2514495
¹H	water	protons	4.705 ppm	internal	direct	1.0
¹⁵N	DSS	methyl protons	0.0 ppm	na	indirect	0.1013291

Referencing offset: 0.02 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	0.0 ppm	na	indirect	0.2514495
¹H	water	protons	4.705 ppm	internal	direct	1.0
¹⁵N	DSS	methyl protons	0.0 ppm	na	indirect	0.1013291

Referencing offset: 0.02 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	0.0 ppm	na	indirect	0.2514495
¹H	water	protons	4.705 ppm	internal	direct	1.0
¹⁵N	DSS	methyl protons	0.0 ppm	na	indirect	0.1013291

Referencing offset: 0.1 ppm, Outliers: 2 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	0.0 ppm	na	indirect	0.2514495
¹H	water	protons	4.705 ppm	internal	direct	1.0
¹⁵N	DSS	methyl protons	0.0 ppm	na	indirect	0.1013291

Referencing offset: 0.12 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2N3F, Strand ID: A Detail

Release date

2015-10-11

Citation

Chemical shift assignments of DRB4 (1-153), a dsRNA binding protein in A. thaliana RNAi pathway
Chiliveri, S.C., Deshmukh, M.V.
Biomol. NMR Assign. (2015), 9, 253-256, PubMed 25281003 , DOI 10.1007/s12104-014-9585-8 , Abstract

Related entities 1. DRB4(1-153), : 1 : 4 : 67 entities Detail

Interaction partners 1. DRB4(1-153), : 3 interactors Detail

More details for 3 interactors identified by 2 citations

Experiments performed 19 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
1	DRB4(1-153)	[U-100% 15N]	0.5 mM
2	Potassium phosphate buffer	natural abundance	50 mM
3	Na2SO4	natural abundance	100 mM
4	DTT	natural abundance	4 mM

2 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
5	DRB4(1-153)	[U-100% 13C; U-100% 15N]	0.5 mM
6	Potassium phosphate buffer	natural abundance	50 mM
7	Na2SO4	natural abundance	100 mM
8	DTT	natural abundance	4 mM

3 3D HN(CA)CO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
5	DRB4(1-153)	[U-100% 13C; U-100% 15N]	0.5 mM
6	Potassium phosphate buffer	natural abundance	50 mM
7	Na2SO4	natural abundance	100 mM
8	DTT	natural abundance	4 mM

4 3D HNCA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
5	DRB4(1-153)	[U-100% 13C; U-100% 15N]	0.5 mM
6	Potassium phosphate buffer	natural abundance	50 mM
7	Na2SO4	natural abundance	100 mM
8	DTT	natural abundance	4 mM

5 3D HN(CO)CA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
5	DRB4(1-153)	[U-100% 13C; U-100% 15N]	0.5 mM
6	Potassium phosphate buffer	natural abundance	50 mM
7	Na2SO4	natural abundance	100 mM
8	DTT	natural abundance	4 mM

6 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
5	DRB4(1-153)	[U-100% 13C; U-100% 15N]	0.5 mM
6	Potassium phosphate buffer	natural abundance	50 mM
7	Na2SO4	natural abundance	100 mM
8	DTT	natural abundance	4 mM

7 3D HN(CO)CACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
5	DRB4(1-153)	[U-100% 13C; U-100% 15N]	0.5 mM
6	Potassium phosphate buffer	natural abundance	50 mM
7	Na2SO4	natural abundance	100 mM
8	DTT	natural abundance	4 mM

8 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
5	DRB4(1-153)	[U-100% 13C; U-100% 15N]	0.5 mM
6	Potassium phosphate buffer	natural abundance	50 mM
7	Na2SO4	natural abundance	100 mM
8	DTT	natural abundance	4 mM

9 3D H(CCO)NH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
5	DRB4(1-153)	[U-100% 13C; U-100% 15N]	0.5 mM
6	Potassium phosphate buffer	natural abundance	50 mM
7	Na2SO4	natural abundance	100 mM
8	DTT	natural abundance	4 mM

10 3D (H)C(CO)NH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
5	DRB4(1-153)	[U-100% 13C; U-100% 15N]	0.5 mM
6	Potassium phosphate buffer	natural abundance	50 mM
7	Na2SO4	natural abundance	100 mM
8	DTT	natural abundance	4 mM

11 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
5	DRB4(1-153)	[U-100% 13C; U-100% 15N]	0.5 mM
6	Potassium phosphate buffer	natural abundance	50 mM
7	Na2SO4	natural abundance	100 mM
8	DTT	natural abundance	4 mM

12 3D HNHA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
5	DRB4(1-153)	[U-100% 13C; U-100% 15N]	0.5 mM
6	Potassium phosphate buffer	natural abundance	50 mM
7	Na2SO4	natural abundance	100 mM
8	DTT	natural abundance	4 mM

13 3D HNHB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
5	DRB4(1-153)	[U-100% 13C; U-100% 15N]	0.5 mM
6	Potassium phosphate buffer	natural abundance	50 mM
7	Na2SO4	natural abundance	100 mM
8	DTT	natural abundance	4 mM

14 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
13	DRB4(1-153)	[U-100% 15N]	0.5 mM
14	Potassium phosphate buffer	natural abundance	50 mM
15	Na2SO4	natural abundance	100 mM
16	DTT	natural abundance	4 mM

15 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
9	DRB4(1-153)	[U-10% 13C; U-100% 15N]	0.5 mM
10	Potassium phosphate buffer	natural abundance	50 mM
11	Na2SO4	natural abundance	100 mM
12	DTT	natural abundance	4 mM

16 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
13	DRB4(1-153)	[U-100% 15N]	0.5 mM
14	Potassium phosphate buffer	natural abundance	50 mM
15	Na2SO4	natural abundance	100 mM
16	DTT	natural abundance	4 mM

17 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
13	DRB4(1-153)	[U-100% 15N]	0.5 mM
14	Potassium phosphate buffer	natural abundance	50 mM
15	Na2SO4	natural abundance	100 mM
16	DTT	natural abundance	4 mM

18 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
1	DRB4(1-153)	[U-100% 15N]	0.5 mM
2	Potassium phosphate buffer	natural abundance	50 mM
3	Na2SO4	natural abundance	100 mM
4	DTT	natural abundance	4 mM

19 3D 1H-13C NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
5	DRB4(1-153)	[U-100% 13C; U-100% 15N]	0.5 mM
6	Potassium phosphate buffer	natural abundance	50 mM
7	Na2SO4	natural abundance	100 mM
8	DTT	natural abundance	4 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_25138_2n3f.nef
Input source #2: Coordindates	2n3f.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
MDHVYKGQLQAYALQHNLELPVYANEREGPPHAPRFRCNVTFCGQTFQSSEFFPTLKSAEHAAAKIAVASLTPQSPEGIDVAYKNLLQEIAQKESSLLPF
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MDHVYKGQLQAYALQHNLELPVYANEREGPPHAPRFRCNVTFCGQTFQSSEFFPTLKSAEHAAAKIAVASLTPQSPEGIDVAYKNLLQEIAQKESSLLPF

-------110-------120-------130-------140-------150---
YATATSGPSHAPTFTSTVEFAGKVFSGEEAKTKKLAEMSAAKVAFMSIKNGNS
|||||||||||||||||||||||||||||||||||||||||||||||||||||
YATATSGPSHAPTFTSTVEFAGKVFSGEEAKTKKLAEMSAAKVAFMSIKNGNS

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	153	0	0	100.0

Content subtype: combined_25138_2n3f.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1504		98.0 (chain: A, length: 153)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	3423 (1)	noe	93.5 (chain: A, length: 153)
2	Distance restraints	CNS/XPLOR_distance_constraints_6	OK	126 (1)	hbond	52.3 (chain: A, length: 153)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	244 (244)	.	89.5 (chain: A, length: 153)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_3	OK	109 (109)	.	71.2 (chain: A, length: 153)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 153, Sequence coverage: 98.0%
- Total number of assignments
  - ¹H chemical shifts: 797
  - ¹³C chemical shifts: 559
  - ¹⁵N chemical shifts: 148
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	904	797	88.2
¹³C chemical shifts	687	559	81.4
¹⁵N chemical shifts	160	148	92.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	304	295	97.0
¹³C chemical shifts	306	300	98.0
¹⁵N chemical shifts	143	139	97.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	600	502	83.7
¹³C chemical shifts	381	259	68.0
¹⁵N chemical shifts	17	9	52.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	80	77	96.3
¹³C chemical shifts	80	70	87.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	80	52	65.0
¹³C chemical shifts	80	0	0.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_4
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 153, Sequence coverage: 93.5%
- Total number of restraints: 3308
- Weight of restraints: 1.0 (3308)
- Potential type of restraints: square-well-parabolic (3308)
- Range of distance target values: 2.0, 4.65 (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_6
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 153, Sequence coverage: 52.3%
  - Total number of restraints: 126
  - Weight of restraints: 1.0 (126)
  - Potential type of restraints: square-well-parabolic (126)
  - Range of distance target values: 2.15, 2.9 (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_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 153, Sequence coverage: 89.5%
- Total number of restraints: 244
- Total number of restraints per polymer type: 244
- Weight of restraints: 1.0 (244)
- Potential type of restraints: square-well-parabolic (244)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_3

Status: OK
Experiment type: .

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 153, Sequence coverage: 71.2%

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
MDHVYKGQLQAYALQHNLELPVYANEREGPPHAPRFRCNVTFCGQTFQSSEFFPTLKSAEHAAAKIAVASLTPQSPEGIDVAYKNLLQEIAQKESSLLPF
   ||  |||  ||   | |  |||||||  || ||||||| ||| ||  ||| |||||    ||||||||| || |||||| |||||| || || || |
...VY..QLQ..AL...L.L..YANEREG..HA.RFRCNVT.CGQ.FQ..EFF.TLKSA....AKIAVASLT.QS.EGIDVA.KNLLQE.AQ.ES.LL.F
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-------110-------120-------130-------140-------150---
YATATSGPSHAPTFTSTVEFAGKVFSGEEAKTKKLAEMSAAKVAFMSIKNGNS
|||||       ||||||||||||||||||||| |||||||||||||||    
YATAT.......TFTSTVEFAGKVFSGEEAKTK.LAEMSAAKVAFMSIK    
-------110-------120-------130-------140---------

Total number of restraints: 109
Potential type of restraints: undefined (109)
Range of observed RDC values: 100.0, -100.0 (Hz)
RDC restraints per residue
- Chain_ID: A
  None

Keywords Arabidopsis thaliana, DCL4, DRB4, RNAi, dsRBD

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.851 seconds)

BMRB: 25138

Sample #1

Sample #2

Sample #3

Sample #4

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. DRB4(1-153), : 1 : 4 : 67 entities Detail

Interaction partners 1. DRB4(1-153), : 3 interactors Detail

Experiments performed 19 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 6 contents Detail