BMRB Entry 30908

Name: Solution NMR structure of the XVIPCD region from the T4SS effector X-Tfe(XAC2609) from Xanthomonas citri
Published: 2021-12-17

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PDB ID: 7mu9
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30908
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution NMR structure of the XVIPCD region from the T4SS effector X-Tfe(XAC2609) from Xanthomonas citri

Deposition date:

2021-05-14

Original release date:

2021-12-17

Authors:

Oka, G.; Salinas, R.; Farah, C.

Citation:

Citation: Oka, Gabriel; Souza, Diorge; Cenens, William; Matsuyama, Bruno; Cardoso, Marcus; Oliveira, Luciana; Lima, Filipe; Cuccovia, Iolanda; Guzzo, Cristiane; Salinas, Roberto; Farah, Chuck. "Structural basis for effector recognition by an antibacterial type IV secretion system" Proc. Natl. Acad. Sci. U. S. A. 119, e2112529119-e2112529119 (2022).
PubMed: 34983846

Assembly members:

Assembly members:
entity_1, polymer, 105 residues, 11480.569 Da.

Natural source:

Natural source: Common Name: Xanthomonas citri Taxonomy ID: 190486 Superkingdom: Bacteria Kingdom: not available Genus/species: Xanthomonas citri

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli BL21(DE3) Vector: pET28a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GSHMSDPRHPDNAMYNGAVS KLEALGERGGFANRKELEQA AGQIVFESKVSGLQRIDHVV PNKSGDGFFAVQGELTDPAM QRVFVDRNQAQNQPLENSSR QAAEE

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list

Data type	Count
13C chemical shifts	355
15N chemical shifts	87
1H chemical shifts	522

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1

Entities:

Entity 1, unit_1 105 residues - 11480.569 Da.

1

GLY

SER

HIS

MET

SER

ASP

PRO

ARG

HIS

PRO

2

ASP

ASN

ALA

MET

TYR

ASN

GLY

ALA

VAL

SER

3

LYS

LEU

GLU

ALA

LEU

GLY

GLU

ARG

GLY

4

PHE

ALA

ASN

ARG

LYS

GLU

LEU

GLU

GLN

ALA

5

ALA

GLY

GLN

ILE

VAL

PHE

GLU

SER

LYS

VAL

6

SER

GLY

LEU

GLN

ARG

ILE

ASP

HIS

VAL

7

PRO

ASN

LYS

SER

GLY

ASP

GLY

PHE

ALA

8

VAL

GLN

GLY

GLU

LEU

THR

ASP

PRO

ALA

MET

9

GLN

ARG

VAL

PHE

VAL

ASP

ARG

ASN

GLN

ALA

10

GLN

ASN

GLN

PRO

LEU

GLU

ASN

SER

ARG

11

GLN

ALA

GLU

Samples:

sample_1: XAC2609(311-411), [U-100% 13C; U-100% 15N], 1.5 mM; TRIS 20 mM; sodium chloride 100 mM; glycerol 0.1 % v/v; sodium azide 0.05 % w/v

sample_conditions_1: ionic strength: 100 mM; pH: 8.0; pressure: 1016 mbar; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D HNCACB	sample_1	anisotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	anisotropic	sample_conditions_1
3D HNCA	sample_1	anisotropic	sample_conditions_1
3D HN(CO)CA	sample_1	anisotropic	sample_conditions_1
3D HNCO	sample_1	anisotropic	sample_conditions_1
HN(CA)CO	sample_1	anisotropic	sample_conditions_1
3D-(H)CCH	sample_1	isotropic	sample_conditions_1
3D-H(C)CH	sample_1	anisotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	anisotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	anisotropic	sample_conditions_1
3D 15N NOESY-HSQC	sample_1	anisotropic	sample_conditions_1
3D 13C NOESY-HSQC	sample_1	anisotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	anisotropic	sample_conditions_1
2D AROMATIC 13C NOESY-HSQC	sample_1	anisotropic	sample_conditions_1
3D (D2O) H(C)CH-TOCSY	sample_1	anisotropic	sample_conditions_1
3D (D2O) (H)CCH-TOCSY	sample_1	anisotropic	sample_conditions_1
3D (D2O) 13C NOESY-HSQC	sample_1	anisotropic	sample_conditions_1
3D (D2) 15N NOESY-HSQC	sample_1	anisotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	anisotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	anisotropic	sample_conditions_1

Software:

CNS, Brunger A. T. et.al. - refinement

ARIA, Linge, O'Donoghue and Nilges - structure calculation

CcpNmr Analysis v2.3, CCPN - chemical shift assignment

NMR spectrometers:

Bruker AVANCE III 800 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks