BMRB Entry 16109
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/BMR16109
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 human ubiquitin-like domain of Herpud2_9_85, Northeast Structural Genomics Consortium (NESG) target HT53A
Deposition date: 2009-01-06 Original release date: 2009-05-26
Authors: Wu, Bin; Yee, Adelinda; Fares, Christophe; Lemak, Alexander; Gutmanas, Aleksandras; Doherty, Ryan; Semesi, Anthony; Dhe-Paganon, Sirano; Arrowsmith, Cheryl
Citation: Doherty, Ryan; Wu, Bin; Fares, Christophe; Lemak, Alexander; Gutmanas, Aleksandras; Semesi, Anthony; Yee, Adelinda; Arrowsmith, Cheryl; Dhe-Paganon, Sirano. "Structure of human homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 2 (Herpud2 or Herp)" Not known ., .-..
Assembly members:
humna_ubiquitin-like_domain_of_Herp, polymer, 99 residues, 9000.604 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):
humna_ubiquitin-like_domain_of_Herp: MGSSHHHHHHSSGRENLYFQ
GHPVTLIIKAPNQKYSDQTI
SCFLNWTVGKLKTHLSNVYP
SKPLTKDQRLVYSGRLLPDH
LQLKDILRKQDEYHMVHLV
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 349 |
| 15N chemical shifts | 73 |
| 1H chemical shifts | 580 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | humna_ubiquitin-like_domain_of_Herp | 1 |
Entities:
Entity 1, humna_ubiquitin-like_domain_of_Herp 99 residues - 9000.604 Da.
| 1 | MET | GLY | SER | SER | HIS | HIS | HIS | HIS | HIS | HIS | ||||
| 2 | SER | SER | GLY | ARG | GLU | ASN | LEU | TYR | PHE | GLN | ||||
| 3 | GLY | HIS | PRO | VAL | THR | LEU | ILE | ILE | LYS | ALA | ||||
| 4 | PRO | ASN | GLN | LYS | TYR | SER | ASP | GLN | THR | ILE | ||||
| 5 | SER | CYS | PHE | LEU | ASN | TRP | THR | VAL | GLY | LYS | ||||
| 6 | LEU | LYS | THR | HIS | LEU | SER | ASN | VAL | TYR | PRO | ||||
| 7 | SER | LYS | PRO | LEU | THR | LYS | ASP | GLN | ARG | LEU | ||||
| 8 | VAL | TYR | SER | GLY | ARG | LEU | LEU | PRO | ASP | HIS | ||||
| 9 | LEU | GLN | LEU | LYS | ASP | ILE | LEU | ARG | LYS | GLN | ||||
| 10 | ASP | GLU | TYR | HIS | MET | VAL | HIS | LEU | VAL |
Samples:
sample_1: humna ubiquitin-like domain of Herp, [U-100% 13C; U-100% 15N], 0.5 mM; TRIS, [U-100% 2H], 10 mM; sodium chloride 300 mM; sodium azide 0.01%; benzamidine 10 mM; H2O 90%; D2O 10%
sample_2: humna ubiquitin-like domain of Herp, [U-100% 13C; U-100% 15N], 0.5 mM; TRIS, [U-100% 2H], 10 mM; sodium chloride 300 mM; sodium azide 0.01%; benzamidine 10 mM; D2O 100%
sample_3: humna ubiquitin-like domain of Herp, [U-7% 13C; U-100% 15N], 0.5 mM; TRIS, [U-100% 2H], 10 mM; sodium chloride 300 mM; sodium azide 0.01%; benzamidine 10 mM; H2O 90%; D2O 10%
sample_conditions_1: ionic strength: 300 mM; pH: 7; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 3D HNCO | sample_1 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HBHA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCA | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 3D CCH-TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY | sample_2 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aromatic | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | sample_3 | isotropic | sample_conditions_1 |
Software:
MNRPipe v2.3, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
SPARKY v3.95, Goddard - data analysis, peak picking
FAWN v1.0, Lemak and Arrowsmith - backbone assignment
CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution
CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement
AutoStruct, Huang, Tejero, Powers and Montelione - NMR structure quality assessment
NMR spectrometers:
- Bruker Avance 600 MHz
- Bruker Avance 800 MHz
- Varian INOVA 500 MHz
Related Database Links:
| PDB | |
| DBJ | BAA95064 BAB31889 BAE22730 BAE89340 BAG38050 |
| GB | AAH05091 AAH20264 AAH29691 AAH43693 AAH81861 |
| REF | NP_001020159 NP_001069026 NP_001270669 NP_065611 NP_071768 |
| SP | Q0P5H8 Q66HH4 Q9BSE4 Q9JJC9 |
| TPG | DAA30580 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts