BMRBj - BMREntryMaster

Found 1 Document (0.713 seconds)

BMRB: 30551

6NE8

Solution Structure of the Thioredoxin-like Domain of Arabidopsis NCP

Authors

Liu, J., Chen, M., Zhou, P.

Assembly

Thioredoxin-like fold domain-containing protein MRL7L, chloroplastic

Entity

1. Thioredoxin-like fold domain-containing protein MRL7L, chloroplastic (polymer), 146 monomers, 16584.05 Da Detail

SHMDNYIRPI KDLTTAEWEE AVFKDISPLM VLVHNRYKRP KENEKFREEL EKAIQVIWNC GLPSPRCVAV DAVVETDLVS ALKVSVFPEI IFTKAGKILY REKGIRTADE LSKIMAFFYY GAAKPPCLNG VVNSQEQIPL VDVSVN

Formula weight

16584.05 Da

Source organism

Arabidopsis thaliana

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.9 %, Completeness: 87.5 %, Completeness (bb): 82.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	87.5 % (1531 of 1750)	95.1 % (866 of 911)	75.9 % (524 of 690)	94.6 % (141 of 149)
Backbone	82.6 % (709 of 858)	96.2 % (277 of 288)	69.5 % (301 of 433)	95.6 % (131 of 137)
Sidechain	92.7 % (958 of 1033)	94.5 % (589 of 623)	90.2 % (359 of 398)	83.3 % (10 of 12)
Aromatic	73.5 % (97 of 132)	92.4 % (61 of 66)	53.1 % (34 of 64)	100.0 % (2 of 2)
Methyl	98.9 % (182 of 184)	97.8 % (90 of 92)	100.0 % (92 of 92)

1. entity 1

SHMDNYIRPI KDLTTAEWEE AVFKDISPLM VLVHNRYKRP KENEKFREEL EKAIQVIWNC GLPSPRCVAV DAVVETDLVS ALKVSVFPEI IFTKAGKILY REKGIRTADE LSKIMAFFYY GAAKPPCLNG VVNSQEQIPL VDVSVN

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 7, Details 1.2 mM [U-99% 13C; U-99% 15N] NCP Thioredoxin-like Domain, 25 mM HEPES, 50 mM KCl (pH 7.0), 10 mM DTT, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	NCP Thioredoxin-like Domain	[U-99% 13C; U-99% 15N]	1.2 mM
2	HEPES	natural abundance	25 mM
3	KCl	natural abundance	50 mM
4	DTT	natural abundance	10 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 7, Details 1.2 mM [U-99% 13C; U-99% 15N] NCP Thioredoxin-like Domain, 25 mM HEPES, 50 mM KCl (pH 7.0), 10 mM DTT, 100% D2O

#	Name	Isotope labeling	Concentration
5	NCP Thioredoxin-like Domain	[U-99% 13C; U-99% 15N]	1.2 mM
6	HEPES	natural abundance	25 mM
7	KCl	natural abundance	50 mM
8	DTT	natural abundance	10 mM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 7, Details 1.2 mM [U-99% 15N] NCP Thioredoxin-like Domain, 25 mM HEPES, 50 mM KCl (pH 7.0), 10 mM DTT, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
9	NCP Thioredoxin-like Domain	[U-99% 15N]	1.2 mM
10	HEPES	natural abundance	25 mM
11	KCl	natural abundance	50 mM
12	DTT	natural abundance	10 mM

LACS Plot; CA

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

Referencing offset: 0.16 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: 0.16 ppm, Outliers: 1 Detail

LACS Plot; HA

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

Referencing offset: 0.01 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 6NE8, Strand ID: A Detail

Release date

2019-02-14

Citation

NCP activates chloroplast transcription by controlling phytochrome-dependent dual nuclear and plastidial switches
Yang, E.J., Yoo, C.Y., Liu, J., Wang, H., Cao, J., Li, F.W., Pryer, K.M., Sun, T.P., Weigel, D., Zhou, P., Chen, M.
Nat. Commun. (2019), 10, 2630-2630, PubMed 31201314 , DOI 10.1038/s41467-019-10517-1 , Abstract

Related entities 1. Thioredoxin-like fold domain-containing protein MRL7L, chloroplastic, : 1 : 2 : 10 entities Detail

Experiments performed 6 experiments Detail

1 Triple-resonance

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 7, Details 1.2 mM [U-99% 13C; U-99% 15N] NCP Thioredoxin-like Domain, 25 mM HEPES, 50 mM KCl (pH 7.0), 10 mM DTT, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	NCP Thioredoxin-like Domain	[U-99% 13C; U-99% 15N]	1.2 mM
2	HEPES	natural abundance	25 mM
3	KCl	natural abundance	50 mM
4	DTT	natural abundance	10 mM

2 4D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	NCP Thioredoxin-like Domain	[U-99% 13C; U-99% 15N]	1.2 mM
2	HEPES	natural abundance	25 mM
3	KCl	natural abundance	50 mM
4	DTT	natural abundance	10 mM

3 4D HCCONH

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	NCP Thioredoxin-like Domain	[U-99% 13C; U-99% 15N]	1.2 mM
2	HEPES	natural abundance	25 mM
3	KCl	natural abundance	50 mM
4	DTT	natural abundance	10 mM

4 3D 1H-15N NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 7, Details 1.2 mM [U-99% 15N] NCP Thioredoxin-like Domain, 25 mM HEPES, 50 mM KCl (pH 7.0), 10 mM DTT, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
9	NCP Thioredoxin-like Domain	[U-99% 15N]	1.2 mM
10	HEPES	natural abundance	25 mM
11	KCl	natural abundance	50 mM
12	DTT	natural abundance	10 mM

5 4D 13C-HMQC-NOESY-15N-HSQC

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	NCP Thioredoxin-like Domain	[U-99% 13C; U-99% 15N]	1.2 mM
2	HEPES	natural abundance	25 mM
3	KCl	natural abundance	50 mM
4	DTT	natural abundance	10 mM

6 4D 13C-HMQC-NOESY-13C-HSQC

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 7, Details 1.2 mM [U-99% 13C; U-99% 15N] NCP Thioredoxin-like Domain, 25 mM HEPES, 50 mM KCl (pH 7.0), 10 mM DTT, 100% D2O

#	Name	Isotope labeling	Concentration
5	NCP Thioredoxin-like Domain	[U-99% 13C; U-99% 15N]	1.2 mM
6	HEPES	natural abundance	25 mM
7	KCl	natural abundance	50 mM
8	DTT	natural abundance	10 mM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr30551_3.str
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

Content subtype: bmr30551_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1700		97.9 (chain: 1, length: 146)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 146, Sequence coverage: 97.9%
- Total number of assignments
  - ¹H chemical shifts: 1058
  - ¹³C chemical shifts: 503
  - ¹⁵N chemical shifts: 139
- Completeness of assignments
  - Entity_assemble_ID: 1
- 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: 1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	911	870	95.5
¹³C chemical shifts	690	503	72.9
¹⁵N chemical shifts	156	139	89.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	288	278	96.5
¹³C chemical shifts	292	143	49.0
¹⁵N chemical shifts	137	130	94.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	623	592	95.0
¹³C chemical shifts	398	360	90.5
¹⁵N chemical shifts	19	9	47.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	95	94	98.9
¹³C chemical shifts	95	94	98.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	66	61	92.4
¹³C chemical shifts	64	34	53.1
¹⁵N chemical shifts	2	2	100.0

Keywords NCP, PLANT PROTEIN, chloroplast biogenesis, phytochrome signaling, plastid-encoded RNA polymerase, thioredoxin-like domain

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Found 1 Document (0.713 seconds)

BMRB: 30551

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Thioredoxin-like fold domain-containing protein MRL7L, chloroplastic, : 1 : 2 : 10 entities Detail

Experiments performed 6 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Chemical shift validation 3 contents Detail