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Biological Magnetic Resonance Data Bank


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BMRB Entry 34817

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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/BMR34817
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Title: bacteriophage T5 l-alanoyl-d-glutamate peptidase Zn2+/Ca2+ form

Deposition date: 2023-05-17 Original release date: 2023-07-04

Authors: Prokhorov, D.; Kutyshenko, V.; Mikoulinskaia, G.

Citation: Prokhorov, D.; Mikoulinskaia, G.; Molochkov, N.; Uversky, V.; Kutyshenko, V.. "Mechanism of Ca2+-dependent activation of L-alanoyl-D-glutamate peptidase bacteriophage T5."  .

Assembly members:
entity_1, polymer, 137 residues, 15286.202 Da.
entity_ZN, non-polymer, 65.409 Da.
entity_CA, non-polymer, 40.078 Da.

Natural source:   Common Name: Escherichia phage T5   Taxonomy ID: 2695836   Superkingdom: Viruses   Kingdom: not available   Genus/species: Tequintavirus Escherichia phage T5

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

Entity Sequences (FASTA):
entity_1: MSFKFGKNSEKQLATVKPEL QKVARRALELSPYDFTIVQG IRTVAQSAQNIANGTSFLKD PSKSKHITGDAIDFAPYING KIDWNDLEAFWAVKKAFEQA GKELGIKLRFGADWNASGDY HDEIKRGTYDGGHVELV

Data sets:
Data typeCount
13C chemical shifts607
15N chemical shifts141
1H chemical shifts569

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1unit_11
2unit_22
3unit_33

Entities:

Entity 1, unit_1 137 residues - 15286.202 Da.

1   METSERPHELYSPHEGLYLYSASNSERGLU
2   LYSGLNLEUALATHRVALLYSPROGLULEU
3   GLNLYSVALALAARGARGALALEUGLULEU
4   SERPROTYRASPPHETHRILEVALGLNGLY
5   ILEARGTHRVALALAGLNSERALAGLNASN
6   ILEALAASNGLYTHRSERPHELEULYSASP
7   PROSERLYSSERLYSHISILETHRGLYASP
8   ALAILEASPPHEALAPROTYRILEASNGLY
9   LYSILEASPTRPASNASPLEUGLUALAPHE
10   TRPALAVALLYSLYSALAPHEGLUGLNALA
11   GLYLYSGLULEUGLYILELYSLEUARGPHE
12   GLYALAASPTRPASNALASERGLYASPTYR
13   HISASPGLUILELYSARGGLYTHRTYRASP
14   GLYGLYHISVALGLULEUVAL

Entity 2, unit_2 - Zn - 65.409 Da.

1   ZN

Entity 3, unit_3 - Ca - 40.078 Da.

1   CA

Samples:

sample_1: l-alanoyl-d-glutamate peptidase, [U-100% 13C; U-100% 15N], 0.8 ± 0.05 mM; sodium acetate, [U-100% 2H], 50 ± 5 mM; Zn(NO3)2 3 ± 0.05 mM; CaCl2 3 ± 0.05 mM; sodium azide 0.03 ± 0.003 %

sample_conditions_1: ionic strength: 50 mM; pH: 4.1; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D 1H-15N TOCSYsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
2D CBHDsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1

Software:

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - refinement, structure calculation

CARA vRelease: 1.8.4.2, Keller and Wuthrich - chemical shift assignment

TopSpin v2.1, Bruker Biospin - peak picking, processing

NMR spectrometers:

  • Bruker AVANCE III 600 MHz

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