BMRB Entry 19872
Click here to enlarge.
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/BMR19872
MolProbity Validation Chart
NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
NMR-STAR v2.1 text file (deprecated)
XML gzip file.
RDF gzip file.
All files associated with the entry
Title: Solution structure of the apo form of human glutaredoxin 5 PubMed: 24733926
Deposition date: 2014-03-25 Original release date: 2015-06-05
Authors: Banci, Lucia; Brancaccio, Diego; Ciofi-Baffoni, Simone; Del Conte, Rebecca; Gadepalli, Ravisekhar; Mikolajczyk, Maciej; Neri, Sara; Piccioli, Mario; Winkelmann, Julia
Citation: Banci, Lucia; Brancaccio, Diego; Ciofi-Baffoni, Simone; Del Conte, Rebecca; Gadepalli, Ravisekhar; Mikolajczyk, Maciej; Neri, Sara; Piccioli, Mario; Winkelmann, Julia. "[2Fe-2S] cluster transfer in iron-sulfur protein biogenesis" Proc. Natl. Acad. Sci. U.S.A. 111, 6203-6208 (2014).
Assembly members:
entity, polymer, 121 residues, 13171.006 Da.
Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
entity: GSFTMGAGGGGSAEQLDALV
KKDKVVVFLKGTPEQPQCGF
SNAVVQILRLHGVRDYAAYN
VLDDPELRQGIKDYSNWPTI
PQVYLNGEFVGGCDILLQMH
QNGDLVEELKKLGIHSALLD
E
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 484 |
| 15N chemical shifts | 118 |
| 1H chemical shifts | 663 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | apo glutaredoxin 5 | 1 |
Entities:
Entity 1, apo glutaredoxin 5 121 residues - 13171.006 Da.
Residues 1-5 represent a non-native cloning artefact.
| 1 | GLY | SER | PHE | THR | MET | GLY | ALA | GLY | GLY | GLY | ||||
| 2 | GLY | SER | ALA | GLU | GLN | LEU | ASP | ALA | LEU | VAL | ||||
| 3 | LYS | LYS | ASP | LYS | VAL | VAL | VAL | PHE | LEU | LYS | ||||
| 4 | GLY | THR | PRO | GLU | GLN | PRO | GLN | CYS | GLY | PHE | ||||
| 5 | SER | ASN | ALA | VAL | VAL | GLN | ILE | LEU | ARG | LEU | ||||
| 6 | HIS | GLY | VAL | ARG | ASP | TYR | ALA | ALA | TYR | ASN | ||||
| 7 | VAL | LEU | ASP | ASP | PRO | GLU | LEU | ARG | GLN | GLY | ||||
| 8 | ILE | LYS | ASP | TYR | SER | ASN | TRP | PRO | THR | ILE | ||||
| 9 | PRO | GLN | VAL | TYR | LEU | ASN | GLY | GLU | PHE | VAL | ||||
| 10 | GLY | GLY | CYS | ASP | ILE | LEU | LEU | GLN | MET | HIS | ||||
| 11 | GLN | ASN | GLY | ASP | LEU | VAL | GLU | GLU | LEU | LYS | ||||
| 12 | LYS | LEU | GLY | ILE | HIS | SER | ALA | LEU | LEU | ASP | ||||
| 13 | GLU |
Samples:
sample_1: apo glutaredoxin 5, [U-100% 15N], 0.5 – 1 mM; potassium phosphate 50 mM; DTT 5 mM; GSH 5 mM; D2O 90%; H2O 10%
sample_2: apo glutaredoxin 5, [U-100% 13C; U-100% 15N], 0.5 – 1 mM; potassium phosphate 50 mM; DTT 5 mM; GSH 5 mM; D2O 90%; H2O 10%
sample_conditions_1: ionic strength: 50 mM; pH: 7; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | sample_2 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_2 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_2 | isotropic | sample_conditions_1 |
| 3D HNCA | sample_2 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_2 | isotropic | sample_conditions_1 |
| 3D HBHA(CO)NH | sample_2 | isotropic | sample_conditions_1 |
| 3D HN(CO)CA | sample_2 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aliphatic | sample_2 | isotropic | sample_conditions_1 |
| 3D HN(CA)CO | sample_2 | isotropic | sample_conditions_1 |
Software:
TOPSPIN, Bruker Biospin - collection, processing
CARA v2.0, Keller and Wuthrich - chemical shift assignment
ATNOS, Herrmann, Guntert and Wuthrich - peak picking
CANDID, Herrmann, Guntert and Wuthrich - automatic noes assignment
TALOS, Cornilescu, Delaglio and Bax - backbone torsion angle calculation
CYANA, Guntert, Mumenthaler and Wuthrich - structure solution
XEASY, Bartels et al. - data analysis
AMBER, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement
PSVS, Bhattacharya and Montelione - structure validation
CING, Vuister, Sousa da Silva, and Doreleijers - structure validation
Molmol, Koradi, Billeter and Wuthrich - data analysis
NMR spectrometers:
- Bruker Avance 500 MHz
- Bruker Avance 700 MHz
- Bruker Avance 800 MHz
- Bruker Avance 900 MHz
Related Database Links:
| PDB | |
| DBJ | BAF02301 |
| EMBL | CAD62364 |
| GB | AAH23528 AAH47680 AAZ30731 EAW81607 EDL18773 |
| REF | NP_001252564 NP_057501 XP_001154482 XP_002754322 XP_002825117 |
| SP | Q86SX6 |