BMRB Entry 34121

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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/BMR34121
MolProbity Validation Chart

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Title:
NMR solution structure of lysostaphin
Deposition date:
2017-04-07
Original release date:
2018-05-10
Authors:
Tossavainen, H.; Raulinaitis, V.; Permi, P.
Citation:

Citation: Tossavainen, Helena; Raulinaitis, Vytas; Kauppinen, Linda; Pentikainen, Ulla; Maaheimo, Hannu; Permi, Perttu. "Structural and Functional Insights Into Lysostaphin-Substrate Interaction"  Front. Mol. Biosci. 5, 60-60 (2018).
PubMed: 30018958

Assembly members:

Assembly members:
entity_1, polymer, 245 residues, 26876.070 Da.
entity_ZN, non-polymer, 65.409 Da.

Natural source:

Natural source:   Common Name: Staphylococcus simulans   Taxonomy ID: 1286   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Staphylococcus simulans

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GSHEHSAQWLNNYKKGYGYG PYPLGINGGMHYGVDFFMNI GTPVKAISSGKIVEAGWSNY GGGNQIGLIENDGVHRQWYM HLSKYNVKVGDYVKAGQIIG WSGSTGYSTAPHLHFQRMVN SFSNSTAQDPMPFLKSAGYG KAGGTVTPTPNTGWKTNKYG TLYKSESASFTPNTDIITRT TGPFRSMPQSGVLKAGQTIH YDEVMKQDGHVWVGYTGNSG QRIYLPVRTWNKSTNTLGVL WGTIK

Data sets:
Data typeCount
13C chemical shifts763
15N chemical shifts245
1H chemical shifts1614

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_22

Entities:

Entity 1, entity_1 245 residues - 26876.070 Da.

1   GLYSERHISGLUHISSERALAGLNTRPLEU
2   ASNASNTYRLYSLYSGLYTYRGLYTYRGLY
3   PROTYRPROLEUGLYILEASNGLYGLYMET
4   HISTYRGLYVALASPPHEPHEMETASNILE
5   GLYTHRPROVALLYSALAILESERSERGLY
6   LYSILEVALGLUALAGLYTRPSERASNTYR
7   GLYGLYGLYASNGLNILEGLYLEUILEGLU
8   ASNASPGLYVALHISARGGLNTRPTYRMET
9   HISLEUSERLYSTYRASNVALLYSVALGLY
10   ASPTYRVALLYSALAGLYGLNILEILEGLY
11   TRPSERGLYSERTHRGLYTYRSERTHRALA
12   PROHISLEUHISPHEGLNARGMETVALASN
13   SERPHESERASNSERTHRALAGLNASPPRO
14   METPROPHELEULYSSERALAGLYTYRGLY
15   LYSALAGLYGLYTHRVALTHRPROTHRPRO
16   ASNTHRGLYTRPLYSTHRASNLYSTYRGLY
17   THRLEUTYRLYSSERGLUSERALASERPHE
18   THRPROASNTHRASPILEILETHRARGTHR
19   THRGLYPROPHEARGSERMETPROGLNSER
20   GLYVALLEULYSALAGLYGLNTHRILEHIS
21   TYRASPGLUVALMETLYSGLNASPGLYHIS
22   VALTRPVALGLYTYRTHRGLYASNSERGLY
23   GLNARGILETYRLEUPROVALARGTHRTRP
24   ASNLYSSERTHRASNTHRLEUGLYVALLEU
25   TRPGLYTHRILELYS

Entity 2, entity_2 - Zn - 65.409 Da.

1   ZN

Samples:

sample_1: lysostaphin, [U-13C; U-15N], 0.36 mM; Bis-Tris 20 mM; ZnCl2 0.36 mM

sample_2: lysostaphin, [U-13C; U-15N], 0.47 mM; Bis-Tris 20 mM; ZnCl2 0.36 mM

sample_conditions_1: ionic strength: 0.15 M; pH: 6.5; pressure: 1 atm; temperature: 308 K

sample_conditions_2: ionic strength: 0.15 M; 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 HNCACBsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
2D (HB)CB(CGCDCE)HEsample_1isotropicsample_conditions_1
2D (HB)CB(CGCD)HDsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_2isotropicsample_conditions_2
3D HCCH-COSYsample_2isotropicsample_conditions_2
3D 1H-13C NOESY aromaticsample_2isotropicsample_conditions_2

Software:

VNMR, Varian - collection, processing

SPARKY, Goddard - data analysis

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

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

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