BMRB Entry 34576

Name: Solution structure of the Pax NRPS docking domain PaxB NDD
Published: 2021-06-02

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PDB ID: 7b2f
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34576
MolProbity Validation Chart

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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 structure of the Pax NRPS docking domain PaxB NDD PubMed: 33675014

Deposition date: 2020-11-26 Original release date: 2021-06-02

Authors: Watzel, J.; Sarawi, S.; Duchardt-Ferner, E.; Bode, H.; Woehnert, J.

Citation: Watzel, J.; Sarawi, S.; Duchardt-Ferner, E.; Bode, H.; Woehnert, J.. "NMR resonance assignments for a docking domain pair with an attached thiolation domain from the PAX peptide-producing NRPS from Xenorhabdus cabanillasii." Biomol. NMR Assign. 15, 229-234 (2021).

Assembly members:
entity_1, polymer, 31 residues, 3616.222 Da.

Natural source: Common Name: Xenorhabdus cabanillasii Taxonomy ID: 1427517 Superkingdom: Bacteria Kingdom: not available Genus/species: Xenorhabdus cabanillasii

Experimental source: Production method: recombinant technology Host organism: Escherichia coli BL21(DE3) Vector: pET-11a

Entity Sequences (FASTA):
entity_1: MNNNELTSLPLAERKRLLEL AKAAKLSRQHY

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list
- spectral_peak_list_1
- spectral_peak_list_2

Data type	Count
13C chemical shifts	134
15N chemical shifts	28
1H chemical shifts	220

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 31 residues - 3616.222 Da.

1

MET

ASN

GLU

LEU

THR

SER

LEU

PRO

2

LEU

ALA

GLU

ARG

LYS

ARG

LEU

GLU

LEU

3

ALA

LYS

ALA

LYS

LEU

SER

ARG

GLN

HIS

4

TYR

Samples:

sample_1: PaxB NDD, [U-15N], 300 uM; sodium phosphate 50 mM; sodium chloride 100 mM; D2O, [U-2H], 5%; DSS 100 uM

sample_2: PaxB NDD, [U-15N], 300 uM; sodium phosphate 50 mM; sodium chloride 100 mM; D2O, [U-2H], 5%; DSS 100 uM

sample_3: PaxB NDD, [U-10% 13C; U-15N], 300 uM; sodium phosphate 50 mM; sodium chloride 100 mM; D2O, [U-2H], 5%; DSS 100 uM

sample_conditions_1: ionic strength: 100 mM; pH: 6.5; pressure: 1 atm; temperature: 293 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_1
3D HNCO	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_3	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_2	isotropic	sample_conditions_1
3D HNCACB	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_2	isotropic	sample_conditions_1
3D H(CCO)NH	sample_2	isotropic	sample_conditions_1
3D C(CO)NH	sample_2	isotropic	sample_conditions_1

Software:

TopSpin v3.6.2, Bruker Biospin - data analysis

CARA v1.8.4.2, Keller and Wuthrich - chemical shift assignment

CcpNmr Analysis v2.4.2, CCPN - peak picking

CYANA v3.98, Guntert, Mumenthaler and Wuthrich - structure calculation

OPALp, Koradi, Billeter and Guntert - refinement

NMR spectrometers:

Bruker AVANCE III HD 800 MHz
Bruker AVANCE II 600 MHz
Bruker AVANCE III HD 700 MHz

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