BMRB Entry 16214

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR16214
MolProbity Validation Chart

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Title:
Zn finger protein YBIL from E.Coli; NESG target ET107; OCSP target EC0402
Deposition date:
2009-03-13
Original release date:
2009-04-14
Authors:
Gutmanas, Aleksandras; Yee, Adelinda; Lemak, Alexander; Fares, Christophe; Guido, Valeria; Arrowsmith, Cheryl
Citation:

Citation: Gutmanas, Aleksandras; Yee, Adelinda; Lemak, Alexander; Fares, Christophe; Arrowsmith, Cheryl. "Zn-finger protein YBIL from E. Coli"  .

Assembly members:

Assembly members:
YBIL, polymer, 108 residues, 9768.879 Da.
ZN, non-polymer, 65.409 Da.

Natural source:

Natural source:   Common Name: E. coli   Taxonomy ID: 62   Superkingdom: Eubacteria   Kingdom: not available   Genus/species: Escherichia coli

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: p11

Entity Sequences (FASTA):

Entity Sequences (FASTA):
YBIL: MGSSHHHHHHSSGLVPRGSH MASGWANDDAVNEQINSTIE DAIARARGEIPRGESLDECE ECGAPIPQARREAIPGVRLC IHCQQEKDLQKPAYTGYNRR GSKDSQLR

Data sets:
Data typeCount
13C chemical shifts349
15N chemical shifts91
1H chemical shifts573

Time Domain Data

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1YBIL1
2ZINC ION2

Entities:

Entity 1, YBIL 108 residues - 9768.879 Da.

1   METGLYSERSERHISHISHISHISHISHIS
2   SERSERGLYLEUVALPROARGGLYSERHIS
3   METALASERGLYTRPALAASNASPASPALA
4   VALASNGLUGLNILEASNSERTHRILEGLU
5   ASPALAILEALAARGALAARGGLYGLUILE
6   PROARGGLYGLUSERLEUASPGLUCYSGLU
7   GLUCYSGLYALAPROILEPROGLNALAARG
8   ARGGLUALAILEPROGLYVALARGLEUCYS
9   ILEHISCYSGLNGLNGLULYSASPLEUGLN
10   LYSPROALATYRTHRGLYTYRASNARGARG
11   GLYSERLYSASPSERGLNLEUARG

Entity 2, ZINC ION - Zn - 65.409 Da.

1   ZN

Samples:

sample_1: entity_1, [U-100% 13C; U-100% 15N], 0.7 – 1 mM; Zn sulfate 10 uM; DTT, [U-2H], 10 mM; TRIS, [U-2H], 10 mM; sodium chloride 300 mM; sodium azide 0.01%; benzamidine 1 mM; Roche inhibitor 1 X; H20 90%; D20 10%

sample_conditions_1: ionic strength: 0.300 M; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
2D 1H-13C CT-HSQCsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D C(CO)NH TOCSYsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D H(CCO)NH TOCSYsample_1isotropicsample_conditions_1
3D H(C)CH-TOCSY aliphaticsample_1isotropicsample_conditions_1
3D (H)CCH-TOCSY aliphaticsample_1isotropicsample_conditions_1
3D 15N-NOESY-HSQCsample_1isotropicsample_conditions_1
3D 13C-NOESY-HSQC aliphaticsample_1isotropicsample_conditions_1
3D 13C-NOESY-HSQC aromaticsample_1isotropicsample_conditions_1
3D H(C)CH-TOCSY aromaticsample_1isotropicsample_conditions_1
2D 1H-15N HSQC long rangesample_1isotropicsample_conditions_1
2D HBCBCGCDHDsample_1isotropicsample_conditions_1
2D HBCBCGCDCEHEsample_1isotropicsample_conditions_1

Software:

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

ABACUS, A. Lemak - chemical shift assignment, data analysis

TALOS, Cornilescu, Delaglio and Bax - geometry optimization

Analysis v2.06, CCPN - data analysis, peak picking

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

MDDNMR, V. Orekhov, I. Ibraghimov - processing

NMR spectrometers:

  • Varian INOVA 600 MHz
  • Bruker Avance 800 MHz

Related Database Links:

PDB
DBJ BAA35469 BAB34304 BAG76383 BAI24246 BAI29690
EMBL CAP75272 CAQ31304 CAQ89806 CAQ97706 CAR02159
GB AAC73890 AAG55175 AAN79361 AAZ87530 ABB60978
REF NP_308908 NP_415324 WP_000135440 WP_000146315 WP_000146334
SP P41039
AlphaFold P41039

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