BMRB Entry 16126

Name: Solution structure of HypA protein
Published: 2009-07-08

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PDB ID: 2kdx
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/BMR16126
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution structure of HypA protein

Deposition date:

2009-01-20

Original release date:

2009-07-08

Authors:

Xia, Wei; Li, Hongyan; Sze, Kong-hung

Citation:

Citation: Xia, Wei; Li, Hongyan; Sze, Kong-hung; Sun, Hongzhe. "Structure of a nickel chaperone, HypA, from Helicobacter pylori reveals two distinct metal binding sites" J. Am. Chem. Soc. 131, 10031-10040 (2009).
PubMed: 19621959

Assembly members:

Assembly members:
HypA, polymer, 119 residues, 13365.460 Da.
ZN, non-polymer, 65.409 Da.

Natural source:

Natural source: Common Name: Helicobacter pylori Taxonomy ID: 210 Superkingdom: Bacteria Kingdom: not available Genus/species: Helicobacter pylori

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
HypA: GSMHEYSVVSSLIALCEEHA KKNQAHKIERVVVGIGERSA MDKSLFVSAFETFREESLVC KDAILDIVDEKVELECKDCS HVFKPNALDYGVCEKCHSKN VIITQGNEMRLLSLEMLAE

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	498
15N chemical shifts	126
1H chemical shifts	813

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	HypA	1
2	Zn	2

Entities:

Entity 1, HypA 119 residues - 13365.460 Da.

1

GLY

SER

MET

HIS

GLU

TYR

SER

VAL

SER

2

SER

LEU

ILE

ALA

LEU

CYS

GLU

HIS

ALA

3

LYS

ASN

GLN

ALA

HIS

LYS

ILE

GLU

ARG

4

VAL

GLY

ILE

GLY

GLU

ARG

SER

ALA

5

MET

ASP

LYS

SER

LEU

PHE

VAL

SER

ALA

PHE

6

GLU

THR

PHE

ARG

GLU

SER

LEU

VAL

CYS

7

LYS

ASP

ALA

ILE

LEU

ASP

ILE

VAL

ASP

GLU

8

LYS

VAL

GLU

LEU

GLU

CYS

LYS

ASP

CYS

SER

9

HIS

VAL

PHE

LYS

PRO

ASN

ALA

LEU

ASP

TYR

10

GLY

VAL

CYS

GLU

LYS

CYS

HIS

SER

LYS

ASN

11

VAL

ILE

THR

GLN

GLY

ASN

GLU

MET

ARG

12

LEU

SER

LEU

GLU

MET

LEU

ALA

GLU

Entity 2, Zn - Zn - 65.409 Da.

1

ZN

Samples:

13C-15N_HypA: HypA, [U-99% 13C; U-99% 15N], 1 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 100 mM; pH: 7.4; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	13C-15N_HypA	isotropic	sample_conditions_1
2D 1H-13C HSQC	13C-15N_HypA	isotropic	sample_conditions_1
3D HNCO	13C-15N_HypA	isotropic	sample_conditions_1
3D HN(CA)CO	13C-15N_HypA	isotropic	sample_conditions_1
3D CBCA(CO)NH	13C-15N_HypA	isotropic	sample_conditions_1
3D HNCACB	13C-15N_HypA	isotropic	sample_conditions_1
3D HCCH-COSY	13C-15N_HypA	isotropic	sample_conditions_1
3D HCCH-TOCSY	13C-15N_HypA	isotropic	sample_conditions_1
3D 1H-15N NOESY	13C-15N_HypA	isotropic	sample_conditions_1
3D 1H-13C NOESY	13C-15N_HypA	isotropic	sample_conditions_1

Software:

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution

AMBER v7.0, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - refinement

NMR spectrometers:

Bruker Avance 600 MHz

PDB	2KDX
DBJ	BAJ55092 BAJ56561 BAJ58417 BAJ59961 BAM96786
EMBL	CAJ99986 CAX29022 CBI66635
GB	AAD06365 AAD07910 ABF84919 ACD47943 ACI27578
REF	NP_207663 WP_000545266 WP_000545267 WP_000545269 WP_000545270
SP	P0A0U4 P0A0U5
AlphaFold	P0A0U4 P0A0U5