BMRB Entry 36001
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR36001
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Title: Structure model of a protein-DNA complex PubMed: 28223353
Deposition date: 2016-06-07 Original release date: 2017-02-20
Authors: Jin, C.; Hu, Y.; Ding, J.; Zhang, Y.
Citation: Guan, Ling; He, Peng; Yang, Fang; Zhang, Yuan; Hu, Yunfei; Ding, Jienv; Hua, Yu; Zhang, Yi; Ye, Qiong; Hu, Jiazhi; Wang, Tao; Jin, Changwen; Kong, Daochun. "Sap1 is a replication-initiation factor essential for the assembly of pre-replicative complex in the fission yeast Schizosaccharomyces pombe" J. Biol. Chem. 292, 6056-6075 (2017).
Assembly members:
entity_1, polymer, 111 residues, 13248.225 Da.
entity_2, polymer, 12 residues, 3638.432 Da.
entity_3, polymer, 12 residues, 3682.424 Da.
Natural source: Common Name: Fission yeast Taxonomy ID: 284812 Superkingdom: Eukaryota Kingdom: Fungi Genus/species: Schizosaccharomyces Schizosaccharomyces pombe
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
entity_1: AKAQRTHLSLEEKIKLMRLV
VRHKHELVDRKTSEFYAKIA
RIGYEDEGLAIHTESACRNQ
IISIMRVYEQRLAHRQPGMK
TTPEEDELDQLCDEWKARLS
ELQQYREKFLV
entity_2: CAAAACAATATT
entity_3: AATATTGTTTTG
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 438 |
| 15N chemical shifts | 98 |
| 1H chemical shifts | 612 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | entity_1 | 1 |
| 2 | entity_2 | 2 |
| 3 | entity_3 | 3 |
Entities:
Entity 1, entity_1 111 residues - 13248.225 Da.
| 1 | ALA | LYS | ALA | GLN | ARG | THR | HIS | LEU | SER | LEU | ||||
| 2 | GLU | GLU | LYS | ILE | LYS | LEU | MET | ARG | LEU | VAL | ||||
| 3 | VAL | ARG | HIS | LYS | HIS | GLU | LEU | VAL | ASP | ARG | ||||
| 4 | LYS | THR | SER | GLU | PHE | TYR | ALA | LYS | ILE | ALA | ||||
| 5 | ARG | ILE | GLY | TYR | GLU | ASP | GLU | GLY | LEU | ALA | ||||
| 6 | ILE | HIS | THR | GLU | SER | ALA | CYS | ARG | ASN | GLN | ||||
| 7 | ILE | ILE | SER | ILE | MET | ARG | VAL | TYR | GLU | GLN | ||||
| 8 | ARG | LEU | ALA | HIS | ARG | GLN | PRO | GLY | MET | LYS | ||||
| 9 | THR | THR | PRO | GLU | GLU | ASP | GLU | LEU | ASP | GLN | ||||
| 10 | LEU | CYS | ASP | GLU | TRP | LYS | ALA | ARG | LEU | SER | ||||
| 11 | GLU | LEU | GLN | GLN | TYR | ARG | GLU | LYS | PHE | LEU | ||||
| 12 | VAL |
Entity 2, entity_2 12 residues - 3638.432 Da.
| 1 | DC | DA | DA | DA | DA | DC | DA | DA | DT | DA | ||||
| 2 | DT | DT |
Entity 3, entity_3 12 residues - 3682.424 Da.
| 1 | DA | DA | DT | DA | DT | DT | DG | DT | DT | DT | ||||
| 2 | DT | DG |
Samples:
sample_1: Sap1, [U-99% 15N][U-99% 13C; U-99% 15N], 0.5 mM; sodium phosphate 20 mM
sample_2: DNA (5'-CAAAACAATATT-3') 0.7 mM; DNA (5'-GTTTTGTTATAA-3') mM; Sap1, [U-99% 13C; U-99% 15N], 0.5 mM; sodium phosphate 20 mM
sample_3: DNA (5'-CAAAACAATATT-3') 0.5 mM; DNA (5'-GTTTTGTTATAA-3') mM; sodium phosphate 20 mM
sample_conditions_1: ionic strength: 60 mM; pH: 6.0; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_2 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY | sample_3 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_2 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_2 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_2 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_2 | isotropic | sample_conditions_1 |
| 3D HNCA | sample_2 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_1 | isotropic | sample_conditions_1 |
| 3D filtered NOESY | sample_2 | isotropic | sample_conditions_1 |
Software:
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
NMRView, Johnson, One Moon Scientific - chemical shift assignment
X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - structure calculation
NMR spectrometers:
- Bruker Avance 500 MHz
- Bruker Avance 800 MHz
- Bruker Avance 950 MHz
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts