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BMRB Entry 25504

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR25504
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Title: Staphylococcus aureus FusB:EF-GC3 complex.   PubMed: 26781961

Deposition date: 2015-02-25 Original release date: 2016-01-25

Authors: Tomlinson, Jennifer; Thompson, Gary; Kalverda, Arnout; Zhuravleva, Anastasia; O'Neill, Alex

Citation: Tomlinson, Jennifer; Thompson, Gary; Kalverda, Arnout; Zhuravleva, Anastasia; O'Neill, Alex. "A target-protection mechanism of antibiotic resistance at atomic resolution: insights into FusB-type fusidic acid resistance"  Sci. Rep. 6, 19524-19524 (2016).

Assembly members:
EF-GC3, polymer, 292 residues, 32272.721 Da.
FusB, polymer, 233 residues, 25225.330 Da.
entity_ZN, non-polymer, 65.409 Da.

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

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

Entity Sequences (FASTA):
EF-GC3: MEFPEPVIHLSVEPKSKADQ DKMTQALVKLQEEDPTFHAH TDEETGQVIIGGMGELHLDI LVDRMKKEFNVECNVGAPMV SYRETFKSSAQVQGKFSRQS GGRGQYGDVHIEFTPNETGA GFEFENAIVGGVVPREYIPS VEAGLKDAMENGVLAGYPLI DVKAKLYDGSYHDVDSSEMA FKIAASLALKEAAKKCDPVI LEPMMKVTIEMPEEYMGDIM GDVTSRRGRVDGMEPRGNAQ VVNAYVPLSEMFGYATSLRS NTQGRGTYTMYFDHYAEVPK SIAEDIIKKNKG
FusB: MGSSHHHHHHSSGLVPNGSH MKTMIYPHQYNYIRSVILRL KNVYKTVNDKETVKVIQSET YNDINEIFGHIDDDIEESLK VLMNIRLSNKEIEAILNKFL EYVVPFELPSPQKLQKVFKK VKKIKIPQFEEYDLKVSSFV GWNELASNRKYIIYYDEKKQ LKGLYGEISNQVVKGFCTIC NKESNVSLFMKKSKTNSDGQ YVKKGDYICRDSIHCNKQLT DINQFYNFIDKLD

Data sets:
Data typeCount
13C chemical shifts246
15N chemical shifts283
1H chemical shifts283

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1EF-GC31
2FusB2
3ZINC ION3

Entities:

Entity 1, EF-GC3 292 residues - 32272.721 Da.

This is a truncated form of the protein comprising domains III-V and beginning at residue 401 of full length EF-G. Residues 694-701 represent a non-native affinity tag.

1   METGLUPHEPROGLUPROVALILEHISLEU
2   SERVALGLUPROLYSSERLYSALAASPGLN
3   ASPLYSMETTHRGLNALALEUVALLYSLEU
4   GLNGLUGLUASPPROTHRPHEHISALAHIS
5   THRASPGLUGLUTHRGLYGLNVALILEILE
6   GLYGLYMETGLYGLULEUHISLEUASPILE
7   LEUVALASPARGMETLYSLYSGLUPHEASN
8   VALGLUCYSASNVALGLYALAPROMETVAL
9   SERTYRARGGLUTHRPHELYSSERSERALA
10   GLNVALGLNGLYLYSPHESERARGGLNSER
11   GLYGLYARGGLYGLNTYRGLYASPVALHIS
12   ILEGLUPHETHRPROASNGLUTHRGLYALA
13   GLYPHEGLUPHEGLUASNALAILEVALGLY
14   GLYVALVALPROARGGLUTYRILEPROSER
15   VALGLUALAGLYLEULYSASPALAMETGLU
16   ASNGLYVALLEUALAGLYTYRPROLEUILE
17   ASPVALLYSALALYSLEUTYRASPGLYSER
18   TYRHISASPVALASPSERSERGLUMETALA
19   PHELYSILEALAALASERLEUALALEULYS
20   GLUALAALALYSLYSCYSASPPROVALILE
21   LEUGLUPROMETMETLYSVALTHRILEGLU
22   METPROGLUGLUTYRMETGLYASPILEMET
23   GLYASPVALTHRSERARGARGGLYARGVAL
24   ASPGLYMETGLUPROARGGLYASNALAGLN
25   VALVALASNALATYRVALPROLEUSERGLU
26   METPHEGLYTYRALATHRSERLEUARGSER
27   ASNTHRGLNGLYARGGLYTHRTYRTHRMET
28   TYRPHEASPHISTYRALAGLUVALPROLYS
29   SERILEALAGLUASPILEILELYSLYSASN
30   LYSGLY

Entity 2, FusB 233 residues - 25225.330 Da.

Residues -19-0 represent a non-native affinity tag.

1   METGLYSERSERHISHISHISHISHISHIS
2   SERSERGLYLEUVALPROASNGLYSERHIS
3   METLYSTHRMETILETYRPROHISGLNTYR
4   ASNTYRILEARGSERVALILELEUARGLEU
5   LYSASNVALTYRLYSTHRVALASNASPLYS
6   GLUTHRVALLYSVALILEGLNSERGLUTHR
7   TYRASNASPILEASNGLUILEPHEGLYHIS
8   ILEASPASPASPILEGLUGLUSERLEULYS
9   VALLEUMETASNILEARGLEUSERASNLYS
10   GLUILEGLUALAILELEUASNLYSPHELEU
11   GLUTYRVALVALPROPHEGLULEUPROSER
12   PROGLNLYSLEUGLNLYSVALPHELYSLYS
13   VALLYSLYSILELYSILEPROGLNPHEGLU
14   GLUTYRASPLEULYSVALSERSERPHEVAL
15   GLYTRPASNGLULEUALASERASNARGLYS
16   TYRILEILETYRTYRASPGLULYSLYSGLN
17   LEULYSGLYLEUTYRGLYGLUILESERASN
18   GLNVALVALLYSGLYPHECYSTHRILECYS
19   ASNLYSGLUSERASNVALSERLEUPHEMET
20   LYSLYSSERLYSTHRASNSERASPGLYGLN
21   TYRVALLYSLYSGLYASPTYRILECYSARG
22   ASPSERILEHISCYSASNLYSGLNLEUTHR
23   ASPILEASNGLNPHETYRASNPHEILEASP
24   LYSLEUASP

Entity 3, ZINC ION - Zn - 65.409 Da.

1   ZN

Samples:

C3_sample_1: EF-GC3, [U-100% 13C; U-100% 15N; partial 2H (grown in D2O with 1H glucose)], 0.250 ± 0.01 mM; FusB 0.375 ± 0.01 mM; TRIS 20 mM; sodium chloride 300 mM; DTT 5 mM

C3_sample_2: EF-GC3, [U-100% 13C; U-100% 15N; partial 2H (grown in D2O with 1H glucose)], 0.250 ± 0.01 mM; FusB 0.375 ± 0.01 mM; TRIS 20 mM; sodium chloride 300 mM; DTT 5 mM; Pf1 phage 6 mg/mL

C3_PRE_sample_1: EF-GC3, [U-100% 13C; U-100% 15N; partial 2H (grown in D2O with 1H glucose)], 0.250 ± 0.01 mM; FusB 0.375 ± 0.01 mM; TRIS 20 mM; sodium chloride 300 mM; DTT 5 mM

C3_PRE_sample_2: EF-GC3, [U-100% 13C; U-100% 15N; partial 2H (grown in D2O with 1H glucose)], 0.250 ± 0.01 mM; FusB 0.375 ± 0.01 mM; TRIS 20 mM; sodium chloride 300 mM; DTT 5 mM

C3_PRE_sample_3: EF-GC3, [U-100% 13C; U-100% 15N; partial 2H (grown in D2O with 1H glucose)], 0.250 ± 0.01 mM; FusB 0.375 ± 0.01 mM; TRIS 20 mM; sodium chloride 300 mM; DTT 5 mM

c3_unlabelled_lys: EF-GC3, [U-100% 15N, partial 2H (grown in D2O with 1H carbon source), 100 % natural abundance lysine], 0.30 ± 0.01 mM; FusB 0.45 ± 0.01 mM; TRIS 20 mM; sodium chloride 300 mM; DTT 5 mM

c3_unlabelled_val: EF-GC3, [U-100% 15N, partial 2H (grown in D2O with 1H carbon source), 100 % natural abundance valine], 0.30 ± 0.01 mM; FusB 0.45 ± 0.01 mM; TRIS 20 mM; sodium chloride 300 mM; DTT 5 mM

c3_unlabelled_phe: EF-GC3, [U-100% 15N, partial 2H (grown in D2O with 1H carbon source), 100 % natural abundance phenylalanine], 0.30 ± 0.01 mM; FusB 0.45 ± 0.01 mM; TRIS 20 mM; sodium chloride 300 mM; DTT 5 mM

c3_unlabelled_ala: EF-GC3, [U-100% 15N, partial 2H (grown in D2O with 1H carbon source), 100 % natural abundance alanine], 0.30 ± 0.01 mM; FusB 0.45 ± 0.01 mM; TRIS 20 mM; sodium chloride 300 mM; DTT 5 mM

c3_unlabelled_asn: EF-GC3, [U-100% 15N, partial 2H (grown in D2O with 1H carbon source), 100 % natural abundance asparagine], 0.30 ± 0.01 mM; FusB 0.45 ± 0.01 mM; TRIS 20 mM; sodium chloride 300 mM; DTT 5 mM

standard_conditions: ionic strength: 0.300 M; pH: 8.000; pressure: 1.000 atm; temperature: 273 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQC/HMQCC3_sample_1isotropicstandard_conditions
3D HNCOC3_sample_1isotropicstandard_conditions
3D HNCAC3_sample_1isotropicstandard_conditions
3D HNCAC3_sample_1isotropicstandard_conditions
3D HN(CO)CAC3_sample_1isotropicstandard_conditions
2D 1H-15N HSQC/HMQCc3_unlabelled_lysisotropicstandard_conditions
2D 1H-15N HSQC/HMQCc3_unlabelled_valisotropicstandard_conditions
2D 1H-15N HSQC/HMQCc3_unlabelled_asnisotropicstandard_conditions
2D 1H-15N HSQC/HMQCc3_unlabelled_pheisotropicstandard_conditions
2D 1H-15N HSQC/HMQCc3_unlabelled_alaisotropicstandard_conditions
2D 1H-15N HSQC/HMQCnot availableisotropicstandard_conditions
2D 1H-15N HSQC/HMQCnot availableisotropicstandard_conditions
2D 1H-15N HSQC/HMQCc3_unlabelled_pheisotropicstandard_conditions
2D 1H-15N HSQC/HMQCc3_unlabelled_valisotropicstandard_conditions
2D 1H-15N HSQC/HMQCnot availableisotropicstandard_conditions
2D 1H-15N HSQC/HMQCnot availableisotropicstandard_conditions
2D 1H-15N HSQC (ARTSY)not availableanisotropicstandard_conditions
2D 1H-15N HSQC (ARTSY)not availableanisotropicstandard_conditions
2D 1H-15N HSQCC3_PRE_sample_1isotropicstandard_conditions
2D 1H-15N HSQCC3_PRE_sample_2isotropicstandard_conditions
2D 1H-15N HSQCC3_PRE_sample_3isotropicstandard_conditions
2D 1H-15N HSQCnot availableisotropicstandard_conditions
2D 1H-15N HSQCnot availableisotropicstandard_conditions
2D 1H-15N HSQC 1H R1 relaxation series (saturation recovery)not availableisotropicstandard_conditions

Software:

CcpNmr_Analysis v2.1, CCPN, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - chemical shift assignment, processing

NMRView v7.9, Johnson, One Moon Scientific - data analysis, processing

X-PLOR_NIH v2.33.0, Schwieters, Kuszewski, Tjandra and Clore - refinement of crystal structure to NMR parameters, structure solution

HADDOCK v2.1, Alexandre Bonvin - docking based on NMR restraints, structure solution

NMR spectrometers:

  • Varian Inova 748 MHz
  • Varian Inova 600 MHz
  • Varian Inova 900 MHz
  • Varian UnityInova 600 MHz

Related Database Links:

NCBI P68790 YP_009078429

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