BMRB Entry 11532
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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/BMR11532
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Title: solution structure of oxidized human HMGB1 A box PubMed: 24513216
Deposition date: 2013-09-12 Original release date: 2014-03-03
Authors: Jing, Wang; Tochio, Naoya; Tate, Shin-ichi
Citation: Jing, Wang; Tochio, Naoya; Tate, Shin-ichi. "Redox-sensitive structural change in the A-domain of HMGB1 and its implication for the binding to cisplatin modified DNA" Biochem. Biophys. Res. Commun. ., .-..
Assembly members:
entity, polymer, 87 residues, 10118.729 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: GSHMGKGDPKKPRGKMSSYA
FFVQTCREEHKKKHPDASVN
FSEFSKKCSERWKTMSAKEK
GKFEDMAKADKARYEREMKT
YIPPKGE
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 398 |
| 15N chemical shifts | 87 |
| 1H chemical shifts | 572 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | entity | 1 |
Entities:
Entity 1, entity 87 residues - 10118.729 Da.
| 1 | GLY | SER | HIS | MET | GLY | LYS | GLY | ASP | PRO | LYS | ||||
| 2 | LYS | PRO | ARG | GLY | LYS | MET | SER | SER | TYR | ALA | ||||
| 3 | PHE | PHE | VAL | GLN | THR | CYS | ARG | GLU | GLU | HIS | ||||
| 4 | LYS | LYS | LYS | HIS | PRO | ASP | ALA | SER | VAL | ASN | ||||
| 5 | PHE | SER | GLU | PHE | SER | LYS | LYS | CYS | SER | GLU | ||||
| 6 | ARG | TRP | LYS | THR | MET | SER | ALA | LYS | GLU | LYS | ||||
| 7 | GLY | LYS | PHE | GLU | ASP | MET | ALA | LYS | ALA | ASP | ||||
| 8 | LYS | ALA | ARG | TYR | GLU | ARG | GLU | MET | LYS | THR | ||||
| 9 | TYR | ILE | PRO | PRO | LYS | GLY | GLU |
Samples:
sample_1: entity, [U-13C; U-15N], 0.5 – 0.6 mM; potassium phosphate 50 mM; potassium chloride 150 mM; D2O, [U-2H], 10%; H2O 90%
sample_2: entity, [U-13C; U-15N], 0.5 – 0.6 mM; C12E5/n-hexanol 6%; potassium chloride 150 mM; potassium phosphate 50 mM; D2O, [U-2H], 10%; H2O 90%
sample_conditions_1: ionic strength: 200 mM; pH: 6.4; pressure: 1 atm; temperature: 293 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 3D 1H-13C NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-15N IPAP-HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-15N IPAP-HSQC | sample_2 | anisotropic | sample_conditions_1 |
Software:
TOPSPIN, Bruker Biospin - collection
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
MAGRO, Kobayashi N. - data analysis
NMRView, Johnson, One Moon Scientific - data analysis
CYANA, Guntert, Mumenthaler and Wuthrich - structure solution
SPARKY, Goddard - data analysis
X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - structure solution
NMR spectrometers:
- Bruker Avance 700 MHz
Related Database Links:
| BMRB | 11147 15148 15149 15502 18709 4079 |
| PDB | |
| DBJ | BAA09924 BAC29902 BAC34367 BAC34773 BAC38678 |
| EMBL | CAA31110 CAA31284 CAA56631 CAA68441 CAA68526 |
| GB | AAA20508 AAA31050 AAA40729 AAA57042 AAA64970 |
| PIR | S29857 |
| REF | NP_001002937 NP_001004034 NP_001075304 NP_001102843 NP_001162380 |
| SP | A9RA84 B0CM99 B1MTB0 P07156 P09429 |
| TPG | DAA21468 DAA23902 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts