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BMRB: 27342

Backbone assignments for the N-terminal domain of VirB10

Authors

Oliveira, L.C., Salinas, R.K., Farah, C.S.

Assembly

VirB10NT

Entity

1. VirB10NT (polymer, Thiol state: not present), 102 monomers, 10505.53 Da Detail

GSHMQSGEDS APPKPRTETV VAPALPQSMT APVEEAPVPL AQQPSLPPLP PMPTDNSEEV SSAPERQRGP TLLERRILAE SAANGGGVPG QLGAQPAPTQ ED

Formula weight

10505.53 Da

Source organism

Xanthomonas citri

Exptl. method

Data set

assigned_chemical_shifts, heteronucl_NOEs

Chem. Shift Complete

Sequence coverage: 97.1 %, Completeness: 53.2 %, Completeness (bb): 79.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	53.2 % (579 of 1089)	20.8 % (120 of 576)	89.8 % (377 of 420)	88.2 % (82 of 93)
Backbone	79.6 % (457 of 574)	46.1 % (89 of 193)	96.0 % (286 of 298)	98.8 % (82 of 83)
Sidechain	34.8 % (212 of 609)	8.1 % (31 of 383)	83.8 % (181 of 216)	0.0 % (0 of 10)
Aromatic	0.0 % (0 of 4)	0.0 % (0 of 2)	0.0 % (0 of 2)
Methyl	42.7 % (41 of 96)	6.3 % (3 of 48)	79.2 % (38 of 48)

1. VirB10NT

GSHMQSGEDS APPKPRTETV VAPALPQSMT APVEEAPVPL AQQPSLPPLP PMPTDNSEEV SSAPERQRGP TLLERRILAE SAANGGGVPG QLGAQPAPTQ ED

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	VirB10NT	[U-100% 13C; U-100% 15N]		300 (±5.0) uM
2	D2O	[U-2H]		10 (±0.1) %
3	sodium acetate	natural abundance		20 (±1.0) mM
4	sodium chloride	natural abundance		150 (±1.0) mM
5	sodium azide	natural abundance		0.05 (±0.001) %

LACS Plot; CA

Referencing offset: -0.06 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.06 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 0.19 ppm, Outliers: 1 Detail

Heteronucl. NOE

62 NOE values in 1 lists
Value type relative intensities, Field strength (¹H) 800 MHz, Pressure 1 atm, Temperature 273 K, pH 5.5 Detail

Release date

2017-12-20

Citation

Cryo-EM structure of the bacteria-killing type IV secretion system core complex from Xanthomonas citri
Sgro, G.G., Costa, T., Cenens, W., Souza, D.P., Cassago, A., Oliveira, L.C., Salinas, R.K., Portugal, R.V., Farah, C.S., Waksman, G.
Nat. Microbiol. (2018), 3, 1429-1440, PubMed 30349081 , DOI 10.1038/s41564-018-0262-z , Abstract

Entries sharing articles EMDB: 1 entries Detail

EMDB: 0089 released on 2018-08-22
Title Cryo-EM structure of the bacteria-killing type IV secretion system core complex from Xanthomonas citri

Experiments performed 9 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance III - 800 MHz The spectrometer is equipped with a cryogenic TCI probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	VirB10NT	[U-100% 13C; U-100% 15N]		300 (±5.0) uM
2	D2O	[U-2H]		10 (±0.1) %
3	sodium acetate	natural abundance		20 (±1.0) mM
4	sodium chloride	natural abundance		150 (±1.0) mM
5	sodium azide	natural abundance		0.05 (±0.001) %

2 3D HNCO

Instrument

Bruker Avance III - 800 MHz The spectrometer is equipped with a cryogenic TCI probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	VirB10NT	[U-100% 13C; U-100% 15N]		300 (±5.0) uM
2	D2O	[U-2H]		10 (±0.1) %
3	sodium acetate	natural abundance		20 (±1.0) mM
4	sodium chloride	natural abundance		150 (±1.0) mM
5	sodium azide	natural abundance		0.05 (±0.001) %

3 3D HNCA

Instrument

Bruker Avance III - 800 MHz The spectrometer is equipped with a cryogenic TCI probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	VirB10NT	[U-100% 13C; U-100% 15N]		300 (±5.0) uM
2	D2O	[U-2H]		10 (±0.1) %
3	sodium acetate	natural abundance		20 (±1.0) mM
4	sodium chloride	natural abundance		150 (±1.0) mM
5	sodium azide	natural abundance		0.05 (±0.001) %

4 3D HNCACB

Instrument

Bruker Avance III - 800 MHz The spectrometer is equipped with a cryogenic TCI probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	VirB10NT	[U-100% 13C; U-100% 15N]		300 (±5.0) uM
2	D2O	[U-2H]		10 (±0.1) %
3	sodium acetate	natural abundance		20 (±1.0) mM
4	sodium chloride	natural abundance		150 (±1.0) mM
5	sodium azide	natural abundance		0.05 (±0.001) %

5 3D CBCA(CO)NH

Instrument

Bruker Avance III - 800 MHz The spectrometer is equipped with a cryogenic TCI probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	VirB10NT	[U-100% 13C; U-100% 15N]		300 (±5.0) uM
2	D2O	[U-2H]		10 (±0.1) %
3	sodium acetate	natural abundance		20 (±1.0) mM
4	sodium chloride	natural abundance		150 (±1.0) mM
5	sodium azide	natural abundance		0.05 (±0.001) %

6 3D CBCA(CO)NH

Instrument

Bruker Avance III - 800 MHz The spectrometer is equipped with a cryogenic TCI probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	VirB10NT	[U-100% 13C; U-100% 15N]		300 (±5.0) uM
2	D2O	[U-2H]		10 (±0.1) %
3	sodium acetate	natural abundance		20 (±1.0) mM
4	sodium chloride	natural abundance		150 (±1.0) mM
5	sodium azide	natural abundance		0.05 (±0.001) %

7 3D C(CO)NH

Instrument

Bruker Avance III - 800 MHz The spectrometer is equipped with a cryogenic TCI probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	VirB10NT	[U-100% 13C; U-100% 15N]		300 (±5.0) uM
2	D2O	[U-2H]		10 (±0.1) %
3	sodium acetate	natural abundance		20 (±1.0) mM
4	sodium chloride	natural abundance		150 (±1.0) mM
5	sodium azide	natural abundance		0.05 (±0.001) %

8 3D HN(CO)CA

Instrument

Bruker Avance III - 800 MHz The spectrometer is equipped with a cryogenic TCI probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	VirB10NT	[U-100% 13C; U-100% 15N]		300 (±5.0) uM
2	D2O	[U-2H]		10 (±0.1) %
3	sodium acetate	natural abundance		20 (±1.0) mM
4	sodium chloride	natural abundance		150 (±1.0) mM
5	sodium azide	natural abundance		0.05 (±0.001) %

9 hsqc_noe_sas_bpp_cpds

Instrument

Bruker Avance III - 800 MHz The spectrometer is equipped with a cryogenic TCI probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 5.5

#	Name	Isotope labeling	Type	Concentration
1	VirB10NT	[U-100% 13C; U-100% 15N]		300 (±5.0) uM
2	D2O	[U-2H]		10 (±0.1) %
3	sodium acetate	natural abundance		20 (±1.0) mM
4	sodium chloride	natural abundance		150 (±1.0) mM
5	sodium azide	natural abundance		0.05 (±0.001) %

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts, Heteronucl NOE exptl data	bmr27342_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: bmr27342_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	OK	537		97.1 (chain: 1, length: 102)
1	Chemical shift references	chemical_shift_reference_1	OK	1		No information

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 102, Sequence coverage: 97.1%
- Total number of assignments
  - ¹³C chemical shifts: 373
  - ¹H chemical shifts: 82
  - ¹⁵N chemical shifts: 82
- Completeness of assignments
  - Entity_assemble_ID: 1
- 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: 1

Keywords T4SS, VirB10