BMRB Entry 34194

Name: Solution Structure of Rhabdopeptide NRPS Docking Domain Kj12B-NDD
Published: 2018-10-24

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PDB ID: 6ewt
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR34194
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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 Rhabdopeptide NRPS Docking Domain Kj12B-NDD

Deposition date:

2017-11-06

Original release date:

2018-10-24

Authors:

Hacker, C.; Cai, X.; Kegler, C.; Zhao, L.; Weickhmann, A.; Bode, H.; Woehnert, J.

Citation:

Citation: Hacker, C.; Cai, X.; Kegler, C.; Zhao, L.; Weickhmann, A.; Bode, H.; Woehnert, J.. "Structure-based redesign of docking domain interactions modulates the product spectrum of a rhabdopeptide-synthesizing NRPS" Nat. Commun. 9, 4366-4366 (2018).
PubMed: 30341296

Assembly members:

Assembly members:
entity_1, polymer, 62 residues, 7245.112 Da.

Natural source:

Natural source: Common Name: Xenorhabdus stockiae Taxonomy ID: 351614 Superkingdom: Bacteria Kingdom: not available Genus/species: Xenorhabdus stockiae

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MKNAAKIVNEALNQGITLFV SDNKLKYKTNRDSIPSELLE EWKQHKQELIDFLTQLESEE ES

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list

Data type	Count
13C chemical shifts	288
15N chemical shifts	70
1H chemical shifts	465

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 62 residues - 7245.112 Da.

1

MET

LYS

ASN

ALA

LYS

ILE

VAL

ASN

GLU

2

ALA

LEU

ASN

GLN

GLY

ILE

THR

LEU

PHE

VAL

3

SER

ASP

ASN

LYS

LEU

LYS

TYR

LYS

THR

ASN

4

ARG

ASP

SER

ILE

PRO

SER

GLU

LEU

GLU

5

GLU

TRP

LYS

GLN

HIS

LYS

GLN

GLU

LEU

ILE

6

ASP

PHE

LEU

THR

GLN

LEU

GLU

SER

GLU

7

GLU

SER

Samples:

sample_1: Kj12BCDD, [U-13C; U-15N], 1 mM; sodium phosphate buffer 50 mM; sodium chloride 100 mM

sample_2: Kj12BCDD, [U-15N], 200 uM; sodium phosphate buffer 50 mM; sodium chloride 100 mM

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

Experiments:

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

Software:

OpalP v3.97, Guenthert - refinement

CARA v3.97, Keller and Wuthrich - chemical shift assignment

Analysis, CCPN - data analysis

TOPSPIN, Bruker Biospin - processing

CANDID, Herrmann, Guntert and Wuthrich - peak picking

CYANA v3.97, Guentert Peter - structure calculation

NMR spectrometers:

Bruker Avance 599 MHz
Bruker Avance 600 MHz

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