BMRB Entry 16126
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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/BMR16126
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Title: Solution structure of HypA protein PubMed: 19621959
Deposition date: 2009-01-20 Original release date: 2009-07-08
Authors: Xia, Wei; Li, Hongyan; Sze, Kong-hung
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).
Assembly members:
HypA, polymer, 119 residues, 13365.460 Da.
ZN, non-polymer, 65.409 Da.
Natural source: Common Name: Helicobacter pylori Taxonomy ID: 210 Superkingdom: Bacteria Kingdom: not available Genus/species: Helicobacter pylori
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
HypA: GSMHEYSVVSSLIALCEEHA
KKNQAHKIERVVVGIGERSA
MDKSLFVSAFETFREESLVC
KDAILDIVDEKVELECKDCS
HVFKPNALDYGVCEKCHSKN
VIITQGNEMRLLSLEMLAE
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 498 |
| 15N chemical shifts | 126 |
| 1H chemical shifts | 813 |
Additional metadata:
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 | VAL | SER | ||||
| 2 | SER | LEU | ILE | ALA | LEU | CYS | GLU | GLU | HIS | ALA | ||||
| 3 | LYS | LYS | ASN | GLN | ALA | HIS | LYS | ILE | GLU | ARG | ||||
| 4 | VAL | VAL | 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 | 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 | ILE | THR | GLN | GLY | ASN | GLU | MET | ARG | ||||
| 12 | LEU | 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
Related Database Links:
| PDB | |
| 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 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts