BMRB Entry 25766

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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/BMR25766
MolProbity Validation Chart

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Title:
Solution structure of Zmp1, a zinc-dependent metalloprotease secreted by Clostridium difficile
Deposition date:
2015-08-24
Original release date:
2016-01-11
Authors:
Banci, Lucia; Cantini, Francesca; Scarselli, Maria; Rubino, Jeff; Martinelli, Manuele
Citation:

Citation: Rubino, Jeff; Martinelli, Manuele; Cantini, Francesca; Banci, Lucia; Scarselli, Maria. "Structural characterization of zinc-bound Zmp1, a zinc-dependent metalloprotease secreted by Clostridium difficile"  J. Biol. Inorg. Chem. 21, 185-196 (2016).
PubMed: 26711661

Assembly members:

Assembly members:
Zmp1, polymer, 195 residues, 21627.457 Da.
ZINC ION, non-polymer, 65.409 Da.
WATER, water, 18.015 Da.

Natural source:

Natural source:   Common Name: firmicutes   Taxonomy ID: 1496   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Clostridium difficile

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET15/TEV

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Zmp1: GDSTTIQQNKDTLSQIVVFP TGNYDKNEANAMVNRLANID GKYLNALKQNNLKIKLLSGK LTDEKEYAYLKGVVPKGWEG TGKTWDDVPGLGGSTVALRI GFSNKGKGHDAINLELHETA HAIDHIVLNDISKSAQFKQI FAKEGRSLGNVNYLGVYPEE FFAESFAYYYLNQDTNSKLK SACPQTYSFLQNLAK

Data sets:
Data typeCount
13C chemical shifts804
15N chemical shifts221
1H chemical shifts1348

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1Zmp11
2ZINC ION2
3HOH3

Entities:

Entity 1, Zmp1 195 residues - 21627.457 Da.

1   GLYASPSERTHRTHRILEGLNGLNASNLYS
2   ASPTHRLEUSERGLNILEVALVALPHEPRO
3   THRGLYASNTYRASPLYSASNGLUALAASN
4   ALAMETVALASNARGLEUALAASNILEASP
5   GLYLYSTYRLEUASNALALEULYSGLNASN
6   ASNLEULYSILELYSLEULEUSERGLYLYS
7   LEUTHRASPGLULYSGLUTYRALATYRLEU
8   LYSGLYVALVALPROLYSGLYTRPGLUGLY
9   THRGLYLYSTHRTRPASPASPVALPROGLY
10   LEUGLYGLYSERTHRVALALALEUARGILE
11   GLYPHESERASNLYSGLYLYSGLYHISASP
12   ALAILEASNLEUGLULEUHISGLUTHRALA
13   HISALAILEASPHISILEVALLEUASNASP
14   ILESERLYSSERALAGLNPHELYSGLNILE
15   PHEALALYSGLUGLYARGSERLEUGLYASN
16   VALASNTYRLEUGLYVALTYRPROGLUGLU
17   PHEPHEALAGLUSERPHEALATYRTYRTYR
18   LEUASNGLNASPTHRASNSERLYSLEULYS
19   SERALACYSPROGLNTHRTYRSERPHELEU
20   GLNASNLEUALALYS

Entity 2, ZINC ION - Zn - 65.409 Da.

1   ZN

Entity 3, HOH - 18.015 Da.

1   HOH

Samples:

sample_1: Zmp1, [U-100% 15N], 0.6 ± 0.2 mM; Zmp1, [U-99% 13C; U-99% 15N], 0.5 ± 0.2 mM; Zmp1 1 ± 0.2 mM; Hepes 20 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 20 mM; pH: 7.2; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HNHAsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1

Software:

CYANA v2.1, Bhattacharya and Montelione, G ntert P. - refinement, structure solution, validation

CYANA v2.1, Bhattacharya and Montelione, G ntert P. - refinement, structure solution, validation

AMBER v10, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

CARA v2, Keller and Wuthrich - data analysis, refinement

TOPSPIN v3, Bruker Biospin - collection

NMR spectrometers:

  • Bruker Avance 950 MHz
  • Bruker Avance 900 MHz
  • Bruker Avance 500 MHz
  • Bruker Avance 700 MHz

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