BMRB Entry 30130

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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/BMR30130
MolProbity Validation Chart

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Title:
Identification and structural characterization of LytU
Deposition date:
2016-07-06
Original release date:
2017-07-26
Authors:
Raulinaitis, V.; Tossavainen, H.; Permi, P.
Citation:

Citation: Raulinaitis, Vytas; Tossavainen, Helena; Aitio, Olli; Juuti, Jarmo; Hiramatsu, Keiichi; Kontinen, Vesa; Permi, Perttu. "Identification and structural characterization of LytU, a unique peptidoglycan endopeptidase from the lysostaphin family"  Sci. Rep. 7, 6020-6020 (2017).
PubMed: 28729697

Assembly members:

Assembly members:
entity_1, polymer, 145 residues, 16272.134 Da.
entity_ZN, non-polymer, 65.409 Da.

Natural source:

Natural source:   Common Name: Staphylococcus aureus   Taxonomy ID: 1280   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Staphylococcus aureus

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GSKWEDFFRGSRITETFGKY QHSPFDGKHYGIDFALPKGT PIKAPTNGKVTRIFNNELGG KVLQIAEDNGEYHQWYLHLD KYNVKVGDRVKAGDIIAYSG NTGIQTTGAHLHFQRMKGGV GNAYAEDPKPFIDQLPDGER SLYDL

Data sets:
Data typeCount
13C chemical shifts474
15N chemical shifts138
1H chemical shifts981

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2ZINC ION2

Entities:

Entity 1, entity_1 145 residues - 16272.134 Da.

1   GLYSERLYSTRPGLUASPPHEPHEARGGLY
2   SERARGILETHRGLUTHRPHEGLYLYSTYR
3   GLNHISSERPROPHEASPGLYLYSHISTYR
4   GLYILEASPPHEALALEUPROLYSGLYTHR
5   PROILELYSALAPROTHRASNGLYLYSVAL
6   THRARGILEPHEASNASNGLULEUGLYGLY
7   LYSVALLEUGLNILEALAGLUASPASNGLY
8   GLUTYRHISGLNTRPTYRLEUHISLEUASP
9   LYSTYRASNVALLYSVALGLYASPARGVAL
10   LYSALAGLYASPILEILEALATYRSERGLY
11   ASNTHRGLYILEGLNTHRTHRGLYALAHIS
12   LEUHISPHEGLNARGMETLYSGLYGLYVAL
13   GLYASNALATYRALAGLUASPPROLYSPRO
14   PHEILEASPGLNLEUPROASPGLYGLUARG
15   SERLEUTYRASPLEU

Entity 2, ZINC ION - Zn - 65.409 Da.

1   ZN

Samples:

sample_1: Bis-Tris buffer 20 mM; LytU, [U-13C; U-15N], 0.5 mM

sample_conditions_1: pH: 6.5; pressure: 1 atm; temperature: 308 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D HN(CO)CACBsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D HCCH-COSYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
2D (HB)CB(CGCDCE)HEsample_1isotropicsample_conditions_1
2D (HB)CB(CGCD)HDsample_1isotropicsample_conditions_1

Software:

AMBER, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

SPARKY, Goddard - chemical shift assignment

VNMRJ, Varian - collection

NMR spectrometers:

  • Varian INOVA 800 MHz

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