BMRB Entry 34257

Name: Solution structure of the Ni metallochaperone HypA from Helicobacter pylori
Published: 2018-10-01

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PDB ID: 6g81
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR34257
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: Solution structure of the Ni metallochaperone HypA from Helicobacter pylori PubMed: 30264175

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: 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).

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

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

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

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

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	516
15N chemical shifts	114
1H chemical shifts	813

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1
2	entity_2	2

Entities:

Entity 1, entity_1 117 residues - 13221.247 Da.

1

MET

HIS

GLU

TYR

SER

VAL

SER

LEU

2

ILE

ALA

LEU

CYS

GLU

HIS

ALA

LYS

3

ASN

GLN

ALA

HIS

LYS

ILE

GLU

ARG

VAL

4

VAL

GLY

ILE

GLY

GLU

ARG

SER

ALA

MET

ASP

5

LYS

SER

LEU

PHE

VAL

SER

ALA

PHE

GLU

THR

6

PHE

ARG

GLU

SER

LEU

VAL

CYS

LYS

ASP

7

ALA

ILE

LEU

ASP

ILE

VAL

ASP

GLU

LYS

VAL

8

GLU

LEU

GLU

CYS

LYS

ASP

CYS

SER

HIS

VAL

9

PHE

LYS

PRO

ASN

ALA

LEU

ASP

TYR

GLY

VAL

10

CYS

GLU

LYS

CYS

HIS

SER

LYS

ASN

VAL

ILE

11

ILE

THR

GLN

GLY

ASN

GLU

MET

ARG

LEU

12

SER

LEU

GLU

MET

LEU

ALA

GLU

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:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D HN(CA)CO	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HBHANH	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_1	isotropic	sample_conditions_1
2D (HB)CB(CGCD)HD	sample_1	isotropic	sample_conditions_1
2D (HB)CB(CGCDCE)HE	sample_1	isotropic	sample_conditions_1
3D HBCB(CGCD)HD	sample_1	isotropic	sample_conditions_1
3D HBCB(CGCDCE)HE	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1
4D 13C(ali)-HMQC-NOESY-13C(aro)-HSQC	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
4D 13C(ali)-HMQC-NOESY-13C(ali)-HMQC	sample_1	isotropic	sample_conditions_1
4D 13C-HMQC-NOESY-15N-HSQC	sample_1	isotropic	sample_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 simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts