BMRB Entry 19731

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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/BMR19731
MolProbity Validation Chart

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Title:
Solution structure of peptidyl-tRNA hyrolase from Vibrio cholerae
Deposition date:
2014-01-11
Original release date:
2015-01-20
Authors:
Kabra, Ashish; Shahid, Salman; Yadav, Rahul; Pulavarti, SV; Shukla, Vaibhav; Arora, Ashish
Citation:

Citation: Kabra, Ashish; Shahid, Salman; Yadav, Rahul; Pulavarti, SV; Shukla, Vaibhav; Arora, Ashish. "Solution structure of peptidyl-tRNA hydrolase from Vibrio cholerae"  .

Assembly members:

Assembly members:
VcPth, polymer, 197 residues, 21616.215 Da.

Natural source:

Natural source:   Common Name: g-proteobacteria   Taxonomy ID: 666   Superkingdom: Bacteria   Kingdom: Proteobacteria   Genus/species: Vibrio cholerae

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET-NH6

Entity Sequences (FASTA):

Entity Sequences (FASTA):
VcPth: MVSQPIKLLVGLANPGPEYA KTRHNAGAWVVEELARIHNV TLKNEPKFFGLTGRLLINSQ ELRVLIPTTFMNLSGKAIAA LANFYQIKPEEIMVAHDELD LPPGVAKFKQGGGHGGHNGL KDTISKLGNNKEFYRLRLGI GHPGHKDKVAGYVLGKAPAK EQECLDAAVDESVRCLEILM KDGLTKAQNRLHTFKAE

Data sets:
Data typeCount
13C chemical shifts826
15N chemical shifts182
1H chemical shifts1287

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity1

Entities:

Entity 1, entity 197 residues - 21616.215 Da.

1   METVALSERGLNPROILELYSLEULEUVAL
2   GLYLEUALAASNPROGLYPROGLUTYRALA
3   LYSTHRARGHISASNALAGLYALATRPVAL
4   VALGLUGLULEUALAARGILEHISASNVAL
5   THRLEULYSASNGLUPROLYSPHEPHEGLY
6   LEUTHRGLYARGLEULEUILEASNSERGLN
7   GLULEUARGVALLEUILEPROTHRTHRPHE
8   METASNLEUSERGLYLYSALAILEALAALA
9   LEUALAASNPHETYRGLNILELYSPROGLU
10   GLUILEMETVALALAHISASPGLULEUASP
11   LEUPROPROGLYVALALALYSPHELYSGLN
12   GLYGLYGLYHISGLYGLYHISASNGLYLEU
13   LYSASPTHRILESERLYSLEUGLYASNASN
14   LYSGLUPHETYRARGLEUARGLEUGLYILE
15   GLYHISPROGLYHISLYSASPLYSVALALA
16   GLYTYRVALLEUGLYLYSALAPROALALYS
17   GLUGLNGLUCYSLEUASPALAALAVALASP
18   GLUSERVALARGCYSLEUGLUILELEUMET
19   LYSASPGLYLEUTHRLYSALAGLNASNARG
20   LEUHISTHRPHELYSALAGLU

Samples:

sample_2: VcPth, [U-100% 13C; U-100% 15N], 0.9 mM; sodium phosphate 20 mM; sodium chloride 50 mM; sodium azide 0.1%; DTT 1 mM; H2O 93%; D2O 7%

sample_1: VcPth, [U-100% 15N], 0.9 mM; sodium phosphate 20 mM; sodium chloride 50 mM; sodium azide 0.1%; DTT 1 mM; H2O 93%; D2O 7%

sample_3: VcPth, [U-100% 13C; U-100% 15N], 0.9 mM; sodium phosphate 20 mM; sodium chloride 50 mM; sodium azide 0.1%; DTT 1 mM; D2O 100%

sample_conditions_1: ionic strength: 50 mM; pH: 6.5; pressure: 1 atm; temperature: 273 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D HNCOsample_2isotropicsample_conditions_1
3D HNCAsample_2isotropicsample_conditions_1
3D CBCA(CO)NHsample_2isotropicsample_conditions_1
3D HNCACBsample_2isotropicsample_conditions_1
3D H(CCO)NHsample_2isotropicsample_conditions_1
3D C(CO)NHsample_2isotropicsample_conditions_1
3D HCCH-TOCSYsample_3isotropicsample_conditions_1
2D 1H-13C HSQCsample_3isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_3isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_3isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_3isotropicsample_conditions_1
3D-HN(CA)COsample_2isotropicsample_conditions_1
2D-CBHEsample_3isotropicsample_conditions_1
2D-CBHDsample_3isotropicsample_conditions_1

Software:

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

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

PSVS, Bhattacharya and Montelione - validation

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

NMR spectrometers:

  • Varian INOVA 600 MHz
  • Bruker Avance 800 MHz

Related Database Links:

PDB
DBJ BAP03589
EMBL CFW05257 CPR23535 CPR23575 CQB51478 CRZ39052
GB AAF95329 ABQ21972 ACP06409 ACP10290 ACQ60361
REF NP_231815 WP_000081939 WP_000081940 WP_000081941 WP_000081943
SP A5F686 C3LPI9 Q9KQ21
AlphaFold C3LPI9 A5F686 Q9KQ21

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