BMRB Entry 25085

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR25085
MolProbity Validation Chart

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Title:
Solution structure of the rhodanese domain of YgaP from E. coli
Deposition date:
2014-07-12
Original release date:
2014-09-19
Authors:
Wang, Wei; Zhou, Peng; Tian, Changlin; Wu, Fangming
Citation:

Citation: Wang, Wei; Zhou, Peng; He, Yao; Yu, Lu; Xiong, Ying; Tian, Changlin; Wu, Fangming. "Fast conformational exchange between the sulfur-free and persulfide-bound rhodanese domain of E. coli YgaP."  Biochem. Biophys. Res. Commun. ., .-. (2014).
PubMed: 25204500

Assembly members:

Assembly members:
YgaP, polymer, 114 residues, 11660.426 Da.

Natural source:

Natural source:   Common Name: E. coli   Taxonomy ID: 562   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Escherichia coli

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: p28

Entity Sequences (FASTA):

Entity Sequences (FASTA):
YgaP: MHHHHHHMALTTISPHDAQE LIARGAKLIDIRDADEYLRE HIPEADLAPLSVLEQSGLPA KLRHEQIIFHCQAGKRTSNN ADKLAAIAAPAEIFLLEDGI DGWKRAGLPVAVNK

Data sets:
Data typeCount
1H chemical shifts724
13C chemical shifts415
15N chemical shifts102

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1rhodanese domain of YgaP1

Entities:

Entity 1, rhodanese domain of YgaP 114 residues - 11660.426 Da.

1   METHISHISHISHISHISHISMETALALEU
2   THRTHRILESERPROHISASPALAGLNGLU
3   LEUILEALAARGGLYALALYSLEUILEASP
4   ILEARGASPALAASPGLUTYRLEUARGGLU
5   HISILEPROGLUALAASPLEUALAPROLEU
6   SERVALLEUGLUGLNSERGLYLEUPROALA
7   LYSLEUARGHISGLUGLNILEILEPHEHIS
8   CYSGLNALAGLYLYSARGTHRSERASNASN
9   ALAASPLYSLEUALAALAILEALAALAPRO
10   ALAGLUILEPHELEULEUGLUASPGLYILE
11   ASPGLYTRPLYSARGALAGLYLEUPROVAL
12   ALAVALASNLYS

Samples:

sample_1: YgaP, [U-100% 13C; U-100% 15N], 0.5 mM; sodium chloride 50 mM; TRIS 20 mM; H2O 90%; D2O 10%

sample_2: YgaP, [U-100% 13C; U-100% 15N], 0.5 mM; sodium chloride 50 mM; TRIS 20 mM; D2O 100%

sample_conditions_1: temperature: 298 K; pH: 7.0; pressure: 1 atm; ionic strength: 0.05 M

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_2isotropicsample_conditions_1
3D HCCH-COSYsample_2isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_1

Software:

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

SPARKY, Goddard - peak picking, chemical shift assignment

X-PLOR_NIH, Schwieters, Kuszewski, Tjandra and Clore - structure solution, refinement

NMR spectrometers:

  • Varian INOVA 700 MHz

Related Database Links:

BMRB 17137 19943 19946
PDB
DBJ BAB36952 BAE76780 BAG78445 BAI26930 BAI31960
EMBL CAQ33005 CAQ87965 CAQ99590 CAR04179 CAR09287
GB AAC75715 AAG57776 AAN44189 AAN81669 AAP18017
REF NP_311556 NP_417154 NP_708482 WP_001229433 WP_001229437
SP P55734
AlphaFold P55734

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