BMRB Entry 34195

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR34195
MolProbity Validation Chart

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Title:
Solution Structure of Rhabdopeptide NRPS Docking Domain Kj12C-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, 63 residues, 7322.091 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: GIDAAQIVDEALEQGITLFV VNNRLQYETSRDSIPTELLN KWKQHKQELIDFLNQLDSEE QTK

Data typeCount
13C chemical shifts274
15N chemical shifts72
1H chemical shifts461

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11

Entities:

Entity 1, entity_1 63 residues - 7322.091 Da.

1   GLYILEASPALAALAGLNILEVALASPGLU
2   ALALEUGLUGLNGLYILETHRLEUPHEVAL
3   VALASNASNARGLEUGLNTYRGLUTHRSER
4   ARGASPSERILEPROTHRGLULEULEUASN
5   LYSTRPLYSGLNHISLYSGLNGLULEUILE
6   ASPPHELEUASNGLNLEUASPSERGLUGLU
7   GLNTHRLYS

Samples:

sample_1: Kj12CDD, [U-15N], 200 uM; sodium phosphate buffer 50 mM; sodium chloride 100 mM

sample_2: Kj12CDD, [U-13C; U-15N], 700 uM; sodium phosphate buffer 50 mM; sodium chloride 100 mM

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

Experiments:

NameSampleSample stateSample conditions
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_2isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_2isotropicsample_conditions_1
3D HNCACBsample_2isotropicsample_conditions_1
3D HNCOsample_2isotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_2isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_2isotropicsample_conditions_1
3D HCCH-TOCSYsample_2isotropicsample_conditions_1
3D HCCH-TOCSYsample_2isotropicsample_conditions_1
3D (H)C(CCO)NHsample_2isotropicsample_conditions_1
3D H(CCO)NHsample_2isotropicsample_conditions_1
3D HBHA(CO)NHsample_2isotropicsample_conditions_1
3D HN(CA)COsample_2isotropicsample_conditions_1

Software:

CYANA v3.97, Guentert - structure calculation

CARA, Keller and Wuthrich - chemical shift assignment

TOPSPIN, Bruker Biospin - collection

Analysis, CCPN - data analysis

UNIO'10 (ATNOS/CANDID, Herrmann, T.; Guentert, P.; Wuethrich, K. J. - peak picking

OPALp, Luginbuhl, Guntert, Billeter and Wuthrich - refinement

NMR spectrometers:

  • Bruker Avance 599 MHz
  • Bruker Avance 600 MHz
  • Bruker Avance 950 MHz
  • Bruker Avance 800 MHz
  • Bruker Avance 800 MHz
  • Bruker Avance 700 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