BMRBj - BMREntryMaster

Found 1 Document (0.573 seconds)

BMRB: 34500

6YDH

Solution structure and dynamics of Zn-Finger HVO_2753 protein

Authors

Kubatova, N., Pyper, D., Schwalbe, H.

Assembly

DUF1610 domain-containing protein

Entity

1. DUF1610 domain-containing protein (polymer), 62 monomers, 6617.470 Da Detail

GAMGSESEQR HAHQCVSCGI NIAGMSAATF KCPDCGQEIS RCSKCRKQSN LYECPDCGFM GP

Formula weight

6617.47 Da

Source organism

Haloferax volcanii

Exptl. method

solution NMR

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 98.4 %, Completeness: 86.8 %, Completeness (bb): 93.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	86.8 % (574 of 661)	82.7 % (286 of 346)	93.5 % (231 of 247)	83.8 % (57 of 68)
Backbone	93.2 % (341 of 366)	86.7 % (111 of 128)	96.6 % (173 of 179)	96.6 % (57 of 59)
Sidechain	82.6 % (289 of 350)	80.7 % (176 of 218)	91.9 % (113 of 123)	0.0 % (0 of 9)
Aromatic	83.3 % (30 of 36)	100.0 % (18 of 18)	66.7 % (12 of 18)
Methyl	100.0 % (32 of 32)	100.0 % (16 of 16)	100.0 % (16 of 16)

1. entity 1

GAMGSESEQR HAHQCVSCGI NIAGMSAATF KCPDCGQEIS RCSKCRKQSN LYECPDCGFM GP

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 278 K, pH 7, Details 1 mM 15N 13C HVO_2753, 25 mM Bis Tris, 200 mM sodium chloride, 3 mM DTT, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	HVO_2753	[U-15N; U-13C]	1 mM
2	Bis Tris	natural abundance	25 mM
3	sodium chloride	natural abundance	200 mM
4	DTT	natural abundance	3 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 278 K, pH 7, Details 1 mM 15N 13C HVO_2753, 25 mM Bis Tris, 200 mM sodium chloride, 3 mM DTT, 100% D2O

#	Name	Isotope labeling	Concentration
5	HVO_2753	[U-15N; U-13C]	1 mM
6	Bis Tris	natural abundance	25 mM
7	sodium chloride	natural abundance	200 mM
8	DTT	natural abundance	3 mM

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 278 K, pH 7, Details 0.5 mM 15N HVO_2753, 25 mM Bis Tris, 200 mM sodium chloride, 3 mM DDT, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
9	HVO_2753	[U-15N]	0.5 mM
10	Bis Tris	natural abundance	25 mM
11	sodium chloride	natural abundance	200 mM
12	DDT	natural abundance	3 mM

Release date

2020-07-13

Citation

Biological functions, genetic and biochemical characterization, and NMR structure determination of the small zinc finger protein HVO_2753 from Haloferax volcanii
Zahn, S., Kubatova, N., Pyper, D.J., Cassidy, L., Saxena, K., Tholey, A., Schwalbe, H., Soppa, J.
FEBS J. (2020), 88, 2042-2062, PubMed 32905660 , DOI 10.1111/febs.15559 , Abstract

Related entities 1. DUF1610 domain-containing protein, : 1 : 9 entities Detail

Experiments performed 19 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AVANCE - 800 MHz cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 278 K, pH 7, Details 1 mM 15N 13C HVO_2753, 25 mM Bis Tris, 200 mM sodium chloride, 3 mM DTT, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	HVO_2753	[U-15N; U-13C]	1 mM
2	Bis Tris	natural abundance	25 mM
3	sodium chloride	natural abundance	200 mM
4	DTT	natural abundance	3 mM

2 2D 1H-13C HSQC

Instrument

Bruker AVANCE - 950 MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
1	HVO_2753	[U-15N; U-13C]	1 mM
2	Bis Tris	natural abundance	25 mM
3	sodium chloride	natural abundance	200 mM
4	DTT	natural abundance	3 mM

3 2D 1H-13C HSQC aromatic

Instrument

Bruker AVANCE - 700 MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
1	HVO_2753	[U-15N; U-13C]	1 mM
2	Bis Tris	natural abundance	25 mM
3	sodium chloride	natural abundance	200 mM
4	DTT	natural abundance	3 mM

4 3D HNCACB

Instrument

Bruker AVANCE - 800 MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
1	HVO_2753	[U-15N; U-13C]	1 mM
2	Bis Tris	natural abundance	25 mM
3	sodium chloride	natural abundance	200 mM
4	DTT	natural abundance	3 mM

5 3D HN(COCA)CB

Instrument

Bruker AVANCE - 800 MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
1	HVO_2753	[U-15N; U-13C]	1 mM
2	Bis Tris	natural abundance	25 mM
3	sodium chloride	natural abundance	200 mM
4	DTT	natural abundance	3 mM

6 3D HN(CA)CO

Instrument

Bruker AVANCE - 800 MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
1	HVO_2753	[U-15N; U-13C]	1 mM
2	Bis Tris	natural abundance	25 mM
3	sodium chloride	natural abundance	200 mM
4	DTT	natural abundance	3 mM

7 3D HNCO

Instrument

Bruker AVANCE - 800 MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
1	HVO_2753	[U-15N; U-13C]	1 mM
2	Bis Tris	natural abundance	25 mM
3	sodium chloride	natural abundance	200 mM
4	DTT	natural abundance	3 mM

8 3D HNHA

Instrument

Bruker AVANCE - 600 MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
1	HVO_2753	[U-15N; U-13C]	1 mM
2	Bis Tris	natural abundance	25 mM
3	sodium chloride	natural abundance	200 mM
4	DTT	natural abundance	3 mM

9 3D (H)CC(CO)NH

Instrument

Bruker AVANCE - 600 MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
1	HVO_2753	[U-15N; U-13C]	1 mM
2	Bis Tris	natural abundance	25 mM
3	sodium chloride	natural abundance	200 mM
4	DTT	natural abundance	3 mM

10 3D 1H-13C TOCSY

Instrument

Bruker AVANCE - 600 MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
1	HVO_2753	[U-15N; U-13C]	1 mM
2	Bis Tris	natural abundance	25 mM
3	sodium chloride	natural abundance	200 mM
4	DTT	natural abundance	3 mM

11 2D 1H-15N HETNOE

Instrument

Bruker AVANCE - 600 MHz cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 278 K, pH 7, Details 0.5 mM 15N HVO_2753, 25 mM Bis Tris, 200 mM sodium chloride, 3 mM DDT, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
9	HVO_2753	[U-15N]	0.5 mM
10	Bis Tris	natural abundance	25 mM
11	sodium chloride	natural abundance	200 mM
12	DDT	natural abundance	3 mM

12 2D 1H-15N T1

Instrument

Bruker AVANCE - 600 MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
9	HVO_2753	[U-15N]	0.5 mM
10	Bis Tris	natural abundance	25 mM
11	sodium chloride	natural abundance	200 mM
12	DDT	natural abundance	3 mM

13 2D 1H-15N T2

Instrument

Bruker AVANCE - 600 MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
9	HVO_2753	[U-15N]	0.5 mM
10	Bis Tris	natural abundance	25 mM
11	sodium chloride	natural abundance	200 mM
12	DDT	natural abundance	3 mM

14 3D HN(CO)CA

Instrument

Bruker AVANCE - 800 MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
1	HVO_2753	[U-15N; U-13C]	1 mM
2	Bis Tris	natural abundance	25 mM
3	sodium chloride	natural abundance	200 mM
4	DTT	natural abundance	3 mM

15 3D 1H-15N TOCSY

Instrument

Bruker AVANCE - 600 MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
1	HVO_2753	[U-15N; U-13C]	1 mM
2	Bis Tris	natural abundance	25 mM
3	sodium chloride	natural abundance	200 mM
4	DTT	natural abundance	3 mM

16 3D CC(CO)NH

Instrument

Bruker AVANCE - 600 MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
1	HVO_2753	[U-15N; U-13C]	1 mM
2	Bis Tris	natural abundance	25 mM
3	sodium chloride	natural abundance	200 mM
4	DTT	natural abundance	3 mM

17 3D 1H-13C NOESY

Instrument

Bruker AVANCE - 950 MHz cryoprobe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 278 K, pH 7, Details 1 mM 15N 13C HVO_2753, 25 mM Bis Tris, 200 mM sodium chloride, 3 mM DTT, 100% D2O

#	Name	Isotope labeling	Concentration
5	HVO_2753	[U-15N; U-13C]	1 mM
6	Bis Tris	natural abundance	25 mM
7	sodium chloride	natural abundance	200 mM
8	DTT	natural abundance	3 mM

18 3D 1H-13C NOESY aromatic

Instrument

Bruker AVANCE - 700 MHz cryoprobe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 278 K, pH 7, Details 1 mM 15N 13C HVO_2753, 25 mM Bis Tris, 200 mM sodium chloride, 3 mM DTT, 100% D2O

#	Name	Isotope labeling	Concentration
5	HVO_2753	[U-15N; U-13C]	1 mM
6	Bis Tris	natural abundance	25 mM
7	sodium chloride	natural abundance	200 mM
8	DTT	natural abundance	3 mM

19 3D 1H-15N NOESY

Instrument

Bruker AVANCE - 950 MHz cryoprobe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 278 K, pH 7, Details 1 mM 15N 13C HVO_2753, 25 mM Bis Tris, 200 mM sodium chloride, 3 mM DTT, 100% D2O

#	Name	Isotope labeling	Concentration
5	HVO_2753	[U-15N; U-13C]	1 mM
6	Bis Tris	natural abundance	25 mM
7	sodium chloride	natural abundance	200 mM
8	DTT	natural abundance	3 mM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34500_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	OK

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Content subtype: bmr34500_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	OK	641		98.4 (chain: 1, length: 62)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 62, Sequence coverage: 98.4%
- Total number of assignments
  - ¹H chemical shifts: 351
  - ¹³C chemical shifts: 234
  - ¹⁵N chemical shifts: 56
- 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	346	319	92.2
¹³C chemical shifts	247	234	94.7
¹⁵N chemical shifts	68	56	82.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	128	123	96.1
¹³C chemical shifts	124	121	97.6
¹⁵N chemical shifts	59	56	94.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	218	196	89.9
¹³C chemical shifts	123	113	91.9
¹⁵N chemical shifts	9	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	19	16	84.2
¹³C chemical shifts	19	16	84.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	18	18	100.0
¹³C chemical shifts	18	12	66.7

Keywords HVO, METAL BINDING PROTEIN, Zn-finger

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Found 1 Document (0.573 seconds)

BMRB: 34500

Sample #1

Sample #2

Sample #3

Related entities 1. DUF1610 domain-containing protein, : 1 : 9 entities Detail

Experiments performed 19 experiments Detail

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Chemical shift validation 3 contents Detail