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Biological Magnetic Resonance Data Bank


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BMRB Entry 25002

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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/BMR25002
MolProbity Validation Chart

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Title: Solution structure of the LysM region of the E. coli Intimin periplasmic domain   PubMed: 25353290

Deposition date: 2014-06-05 Original release date: 2014-11-10

Authors: Coles, Murray; Chaubey, Manish; Leo, Jack; Linke, Dirk; Schuetz, Monika; Goetz, Friedrich; Autenrieth, Ingo

Citation: Leo, Jack; Oberhettinger, Philipp; Chaubey, Manish; Schuetz, Monika; Kuehner, Daniel; Goetz, Friedrich; Coles, Murray; Autenrieth, Ingo; Linke, Dirk. "The intimin periplasmic domain mediates dimerisation and binding to peptidoglycan"  Mol. Microbiol. ., .-. (2014).

Assembly members:
LysM, polymer, 115 residues, 12568.278 Da.

Natural source:   Common Name: E. coli   Taxonomy ID: 562   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Escherichia coli

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli

Entity Sequences (FASTA):
LysM: MNGENYFKLGSDSKLLTHNS YQNRLFYTLKTGETVADLSK SQDINLSTIWSLNKHLYSSE SEMMKAAPGQQIILPLKKLP FEYSALPLLGSAPLVAAGGV AGHTNGSGSENLYFQ

Data sets:
Data typeCount
1H chemical shifts550
13C chemical shifts315
15N chemical shifts82

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1LysM1

Entities:

Entity 1, LysM 115 residues - 12568.278 Da.

A39 is mutated to M for cloning purposes

1   METASNGLYGLUASNTYRPHELYSLEUGLY
2   SERASPSERLYSLEULEUTHRHISASNSER
3   TYRGLNASNARGLEUPHETYRTHRLEULYS
4   THRGLYGLUTHRVALALAASPLEUSERLYS
5   SERGLNASPILEASNLEUSERTHRILETRP
6   SERLEUASNLYSHISLEUTYRSERSERGLU
7   SERGLUMETMETLYSALAALAPROGLYGLN
8   GLNILEILELEUPROLEULYSLYSLEUPRO
9   PHEGLUTYRSERALALEUPROLEULEUGLY
10   SERALAPROLEUVALALAALAGLYGLYVAL
11   ALAGLYHISTHRASNGLYSERGLYSERGLU
12   ASNLEUTYRPHEGLN

Samples:

sample_1: LysM, [U-100% 15N], 0.5 mM; sodium phosphate 20 mM; sodium chloride 150 mM; H2O 90%; D2O 10%

sample_2: LysM, [U-100% 13C; U-100% 15N], 0.5 mM; sodium phosphate 20 mM; sodium chloride 150 mM; H2O 90%; D2O 10%

sample_conditions_1: temperature: 298 K; pH: 7.4; pressure: 1 atm; ionic strength: 250 mM

Experiments:

NameSampleSample stateSample conditions
3D HNCOsample_2isotropicsample_conditions_1
3D HNCAsample_2isotropicsample_conditions_1
3D C(CO)NHsample_2isotropicsample_conditions_1
3D HNCANNHsample_2isotropicsample_conditions_1
3D HCCH-TOCSYsample_2isotropicsample_conditions_1
3D H(CCO)NHsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_1
3D CNH-NOESYsample_2isotropicsample_conditions_1
3D NNH-NOESYsample_1isotropicsample_conditions_1
3D CCH-NOESYsample_2isotropicsample_conditions_1
2D 12C-filtered 1H-1H NOESYsample_1isotropicsample_conditions_1

Software:

TOPSPIN, Bruker Biospin - collection, processing

SPARKY, Goddard - chemical shift assignment, data analysis

X-PLOR_NIH, Schwieters, Kuszewski, Tjandra and Clore - structure solution, refinement

NMR-SPIRIT v1.1, In house - refinement

NMR spectrometers:

  • Bruker Avance 600 MHz
  • Bruker Avance 800 MHz

Related Database Links:

GB BAL46976 AAA62775 AAB52913 AAC31504 AAC38392 AAD05498
PDB
DBJ BAB37982 BAD20939 BAD20940 BAD20941 BAD20942
EMBL CAA42967 CAA77642 CAC21552 CAC24714 CAC59747
PRF 1905283A
REF NP_312586 WP_000430959 WP_000627883 WP_000627884 WP_000627885
SP P19809 P43261

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