BMRB Entry 5209
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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/BMR5209
MolProbity Validation Chart
NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry
Citation: Gryk, Michael; Marintchev, Assen; Maciejewski, Mark; Robertson, Anthony; Wilson, Samuel; Mullen, Gregory. "Mapping of the interaction interface of DNA polymerase beta with XRCC1" Structure 10, 1709-1720 (2002).
PubMed: 12467578
Assembly members:
DNA Polymerase B, polymer, 190 residues, 22022 Da.
XRCC1 N-terminal Domain, polymer, 157 residues, 17358 Da.
Natural source: Common Name: Rat Taxonomy ID: 10116 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Rattus norvegicus
Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET-28a(+)
Entity Sequences (FASTA):
DNA Polymerase B: MGKRIPREEMLQMQDIVLNE
VKKLDPEYIATVCGSFRRGA
ESSGDMDVLLTHPNFTSESS
KQPKLLHRVVEQLQKVRFIT
DTLSKGETKFMGVCQLPSEN
DENEYPHRRIDIRLIPKDQY
YCGVLYFTGSDIFNKNMRAH
ALEKGFTINEYTIRPLGVTG
VAGEPLPVDSEQDIFDYIQW
RYREPKDRSE
XRCC1 N-terminal Domain: MPEIRLRHVVSCSSQDSTHC
AENLLKADTYRKWRAAKAGE
KTISVVLQLEKEEQIHSVDI
GNDGSAFVEVLVGSSAGGAG
EQDYEVLLVTSSFMSPSESR
SGSNPNRVRMFGPDKLVRAA
AEKRWDRVKIVCSQPYSKDS
PFGLSFVRFHSPPDKDE
- assigned_chemical_shifts
| Data type | Count |
| 1H chemical shifts | 332 |
| 13C chemical shifts | 505 |
| 15N chemical shifts | 164 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | B-Pol palm-thumb | 1 |
| 2 | XRCC1-NTD | 2 |
Entities:
Entity 1, B-Pol palm-thumb 190 residues - 22022 Da.
| 1 | MET | GLY | LYS | ARG | ILE | PRO | ARG | GLU | GLU | MET | |
| 2 | LEU | GLN | MET | GLN | ASP | ILE | VAL | LEU | ASN | GLU | |
| 3 | VAL | LYS | LYS | LEU | ASP | PRO | GLU | TYR | ILE | ALA | |
| 4 | THR | VAL | CYS | GLY | SER | PHE | ARG | ARG | GLY | ALA | |
| 5 | GLU | SER | SER | GLY | ASP | MET | ASP | VAL | LEU | LEU | |
| 6 | THR | HIS | PRO | ASN | PHE | THR | SER | GLU | SER | SER | |
| 7 | LYS | GLN | PRO | LYS | LEU | LEU | HIS | ARG | VAL | VAL | |
| 8 | GLU | GLN | LEU | GLN | LYS | VAL | ARG | PHE | ILE | THR | |
| 9 | ASP | THR | LEU | SER | LYS | GLY | GLU | THR | LYS | PHE | |
| 10 | MET | GLY | VAL | CYS | GLN | LEU | PRO | SER | GLU | ASN | |
| 11 | ASP | GLU | ASN | GLU | TYR | PRO | HIS | ARG | ARG | ILE | |
| 12 | ASP | ILE | ARG | LEU | ILE | PRO | LYS | ASP | GLN | TYR | |
| 13 | TYR | CYS | GLY | VAL | LEU | TYR | PHE | THR | GLY | SER | |
| 14 | ASP | ILE | PHE | ASN | LYS | ASN | MET | ARG | ALA | HIS | |
| 15 | ALA | LEU | GLU | LYS | GLY | PHE | THR | ILE | ASN | GLU | |
| 16 | TYR | THR | ILE | ARG | PRO | LEU | GLY | VAL | THR | GLY | |
| 17 | VAL | ALA | GLY | GLU | PRO | LEU | PRO | VAL | ASP | SER | |
| 18 | GLU | GLN | ASP | ILE | PHE | ASP | TYR | ILE | GLN | TRP | |
| 19 | ARG | TYR | ARG | GLU | PRO | LYS | ASP | ARG | SER | GLU |
Entity 2, XRCC1-NTD 157 residues - 17358 Da.
| 1 | MET | PRO | GLU | ILE | ARG | LEU | ARG | HIS | VAL | VAL | ||||
| 2 | SER | CYS | SER | SER | GLN | ASP | SER | THR | HIS | CYS | ||||
| 3 | ALA | GLU | ASN | LEU | LEU | LYS | ALA | ASP | THR | TYR | ||||
| 4 | ARG | LYS | TRP | ARG | ALA | ALA | LYS | ALA | GLY | GLU | ||||
| 5 | LYS | THR | ILE | SER | VAL | VAL | LEU | GLN | LEU | GLU | ||||
| 6 | LYS | GLU | GLU | GLN | ILE | HIS | SER | VAL | ASP | ILE | ||||
| 7 | GLY | ASN | ASP | GLY | SER | ALA | PHE | VAL | GLU | VAL | ||||
| 8 | LEU | VAL | GLY | SER | SER | ALA | GLY | GLY | ALA | GLY | ||||
| 9 | GLU | GLN | ASP | TYR | GLU | VAL | LEU | LEU | VAL | THR | ||||
| 10 | SER | SER | PHE | MET | SER | PRO | SER | GLU | SER | ARG | ||||
| 11 | SER | GLY | SER | ASN | PRO | ASN | ARG | VAL | ARG | MET | ||||
| 12 | PHE | GLY | PRO | ASP | LYS | LEU | VAL | ARG | ALA | ALA | ||||
| 13 | ALA | GLU | LYS | ARG | TRP | ASP | ARG | VAL | LYS | ILE | ||||
| 14 | VAL | CYS | SER | GLN | PRO | TYR | SER | LYS | ASP | SER | ||||
| 15 | PRO | PHE | GLY | LEU | SER | PHE | VAL | ARG | PHE | HIS | ||||
| 16 | SER | PRO | PRO | ASP | LYS | ASP | GLU |
Samples:
sample_1: DNA Polymerase B, [U-98% 13C; U-99% 15N; U-97% 2H; except V g-methyls, L d-methyls, I d-methyl, and labile protons. , $XRCC1-NTD ± 0.8 1.1; 5209, 1, 46; 5209, 1, 135; 5209, 1, 0.002; 5209, 1, 100; 5209, 1, 5; 5209, 1, 90; 5209, 1, 10; 5209, 1,
complex_cond1: pH: 6.8; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D TROSY 1H-15N HSQC | not available | not available | not available |
| 2D 1H-15N HSQC | not available | not available | not available |
| 2D CT 1H-13C HSQC | not available | not available | not available |
| 3D TROSY HNCACB | not available | not available | not available |
| 3D TROSY HNCO | not available | not available | not available |
| 3D (HM)CMC(CM)HM | not available | not available | not available |
| 3D 15N,13C NOESY | not available | not available | not available |
Software:
NMRPipe v1.8 - spectral processing
sbtools - NMR data processing script generation
XEASY v1.2 - spectral analysis
NMR spectrometers:
- Varian INOVA 600 MHz
Related Database Links:
| BMRB | 4282 4282 |
| PDB | |
| DBJ | BAD92018 BAG10574 BAG37732 BAG57023 BAG57023 BAG37732 BAG10574 BAD92018 |
| EMBL | CAG33009 CAG33009 |
| GB | AAA63270 AAH23593 AAM34791 EAW57201 EAW57202 |
| REF | NP_006288 XP_001100256 XP_001499917 XP_002829368 XP_002923977 XP_001499917 XP_001100256 NP_006288 |
| SP | P18887 |
| SWISS-PROT | P18887 |
| GenBank | EAW57202 EAW57201 AAM34791 AAH23593 AAA63270 |
| AlphaFold | P18887 P18887 P18887 P18887 P18887 |
Download HSQC peak lists in one of the following formats:
CSV: Backbone
or all simulated peaks
SPARKY: Backbone
or all simulated peaks