BMRB Entry 36142

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR36142
MolProbity Validation Chart

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Title:
Solution structure of LysM domain from a chitinase derived from Volvox carteri
Deposition date:
2017-12-13
Original release date:
2018-12-17
Authors:
Kitaoku, Y.; Nishimura, S.; Fukamizo, T.; Ohnuma, T.
Citation:

Citation: Kitaoku, Yoshihito; Nishimura, Shigenori; Hirono, Takeru; Suginta, Wipa; Ohnuma, Takayuki; Fukamizo, Tamo. "Structures and chitin-binding properties of two N-terminal lysin motifs (LysMs) found in a chitinase from Volvox carteri."  Glycobiology 29, 565-575 (2019).
PubMed: 30976779

Assembly members:

Assembly members:
entity_1, polymer, 49 residues, 5305.097 Da.

Natural source:

Natural source:   Common Name: Volvox carteri   Taxonomy ID: 3068   Superkingdom: Eukaryota   Kingdom: Viridiplantae   Genus/species: Volvox Volvox carteri

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MGCTYTIQPGDTFWAIAQRR GTTVDVIQSLNPGVVPTRLQ VGQVINVPC

Data sets:
Data typeCount
13C chemical shifts210
15N chemical shifts55
1H chemical shifts337

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 49 residues - 5305.097 Da.

1   METGLYCYSTHRTYRTHRILEGLNPROGLY
2   ASPTHRPHETRPALAILEALAGLNARGARG
3   GLYTHRTHRVALASPVALILEGLNSERLEU
4   ASNPROGLYVALVALPROTHRARGLEUGLN
5   VALGLYGLNVALILEASNVALPROCYS

Samples:

sample_1: LysM, [U-13C; U-15N], 360 uM; sodium acetate, [U-2H], 20 mM; H2O 90%; D2O, [U-2H], 10%

sample_2: LysM, [U-13C; U-15N], 267 uM; sodium acetate, [U-2H], 20 mM; D2O, [U-2H], 100%

sample_conditions_1: ionic strength: 20 mM; pH: 5.0; pressure: 1 atm; temperature: 189 K

sample_conditions_2: ionic strength: 20 mM; pH: 5.0; pressure: 1 atm; temperature: 300 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCACOsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_2
3D HBHACBCACONHsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_2isotropicsample_conditions_2
3D HCCH-TOCSYsample_2isotropicsample_conditions_2
3D CCH-TOCSYsample_2isotropicsample_conditions_2
3D 1H-15N TOCSYsample_1isotropicsample_conditions_1

Software:

CYANA, Guntert P., Guntert, Mumenthaler and Wuthrich - refinement, structure calculation

NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

SPARKY, Goddard - chemical shift assignment, peak picking

TOPSPIN, Bruker Biospin - collection

NMR spectrometers:

  • Bruker AvanceIII 500 MHz

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