BMRB Entry 34257

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR34257
MolProbity Validation Chart

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Title:
Solution structure of the Ni metallochaperone HypA from Helicobacter pylori
Deposition date:
2018-04-07
Original release date:
2018-10-01
Authors:
Spronk, C.; Zerko, S.; Gorka, M.; Kozminski, W.; Bardiaux, B.; Zambelli, B.; Musiani, F.; Piccioli, M.; Hu, H.; Maroney, M.; Ciurli, S.
Citation:

Citation: Spronk, Chris; Zerko, Szymon; Gorka, Michal; Kozminski, Wiktor; Bardiaux, Benjamin; Zambelli, Barbara; Musiani, Francesco; Piccioli, Mario; Basak, Priyanka; Blum, Faith; Johnson, Ryan; Hu, Heidi; Merrell, D Scott; Maroney, Michael; Ciurli, Stefano. "Structure and dynamics of Helicobacter pylori nickel-chaperone HypA: an integrated approach using NMR spectroscopy, functional assays and computational tools"  J. Biol. Inorg. Chem. 23, 1309-1330 (2018).
PubMed: 30264175

Assembly members:

Assembly members:
entity_1, polymer, 117 residues, 13221.247 Da.
entity_ZN, non-polymer, 65.409 Da.

Natural source:

Natural source:   Common Name: Campylobacter pylori J99   Taxonomy ID: 85963   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Helicobacter pylori

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MHEYSVVSSLIALCEEHAKK NQAHKIERVVVGIGERSAMD KSLFVSAFETFREESLVCKD AILDIVDEKVELECKDCSHV FKPNALDYGVCEKCHSKNVI ITQGNEMRLLSLEMLAE

Data sets:
Data typeCount
13C chemical shifts516
15N chemical shifts114
1H chemical shifts813

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_22

Entities:

Entity 1, entity_1 117 residues - 13221.247 Da.

1   METHISGLUTYRSERVALVALSERSERLEU
2   ILEALALEUCYSGLUGLUHISALALYSLYS
3   ASNGLNALAHISLYSILEGLUARGVALVAL
4   VALGLYILEGLYGLUARGSERALAMETASP
5   LYSSERLEUPHEVALSERALAPHEGLUTHR
6   PHEARGGLUGLUSERLEUVALCYSLYSASP
7   ALAILELEUASPILEVALASPGLULYSVAL
8   GLULEUGLUCYSLYSASPCYSSERHISVAL
9   PHELYSPROASNALALEUASPTYRGLYVAL
10   CYSGLULYSCYSHISSERLYSASNVALILE
11   ILETHRGLNGLYASNGLUMETARGLEULEU
12   SERLEUGLUMETLEUALAGLU

Entity 2, entity_2 - Zn - 65.409 Da.

1   ZN

Samples:

sample_1: HypA, [U-13C; U-15N], 1 mM; HEPES 20 mM; sodium chloride 200 mM; TCEP 1 mM

sample_conditions_1: ionic strength: 0.2 M; pH: 7.2; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D HN(CA)COsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HBHANHsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_1isotropicsample_conditions_1
2D (HB)CB(CGCD)HDsample_1isotropicsample_conditions_1
2D (HB)CB(CGCDCE)HEsample_1isotropicsample_conditions_1
3D HBCB(CGCD)HDsample_1isotropicsample_conditions_1
3D HBCB(CGCDCE)HEsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1
4D 13C(ali)-HMQC-NOESY-13C(aro)-HSQCsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
4D 13C(ali)-HMQC-NOESY-13C(ali)-HMQCsample_1isotropicsample_conditions_1
4D 13C-HMQC-NOESY-15N-HSQCsample_1isotropicsample_conditions_1

Software:

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

SSA_software_package, Stanek, Kosinski, Kozminski - processing

CARA, Keller and Wuthrich - chemical shift assignment

SPARKY, Goddard - chemical shift assignment

TALOS+, Cornilescu, Delaglio and Bax - data analysis

YARIA, Bardiaux, Krieger, Spronk - structure calculation

ARIA, Linge, O'Donoghue and Nilges - structure calculation

YASARA, YASARA Biosciences - refinement

NMR spectrometers:

  • Bruker Avance 900 MHz
  • Bruker Avance 950 MHz
  • Agilent DDR2 800 MHz
  • Agilent DDR2 600 MHz

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