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Biological Magnetic Resonance Data Bank


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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

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Title: 1H, 13C and 15N resonance assignments for the perdeuterated 22 kD palm-thumb domain of DNA polymerase B in complex with the XRCC1 N-terminal domain   PubMed: 12467578

Deposition date: 2001-11-14 Original release date: 2005-06-02

Authors: Gryk, Michael; Marintchev, Assen; Maciejewski, Mark; Robertson, Anthony; Mullen, Mary; Wilson, Samuel; Mullen, Gregory

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).

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

Data sets:
Data typeCount
1H chemical shifts332
13C chemical shifts505
15N chemical shifts164

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1B-Pol palm-thumb1
2XRCC1-NTD2

Entities:

Entity 1, B-Pol palm-thumb 190 residues - 22022 Da.

1   METGLYLYSARGILEPROARGGLUGLUMET
2   LEUGLNMETGLNASPILEVALLEUASNGLU
3   VALLYSLYSLEUASPPROGLUTYRILEALA
4   THRVALCYSGLYSERPHEARGARGGLYALA
5   GLUSERSERGLYASPMETASPVALLEULEU
6   THRHISPROASNPHETHRSERGLUSERSER
7   LYSGLNPROLYSLEULEUHISARGVALVAL
8   GLUGLNLEUGLNLYSVALARGPHEILETHR
9   ASPTHRLEUSERLYSGLYGLUTHRLYSPHE
10   METGLYVALCYSGLNLEUPROSERGLUASN
11   ASPGLUASNGLUTYRPROHISARGARGILE
12   ASPILEARGLEUILEPROLYSASPGLNTYR
13   TYRCYSGLYVALLEUTYRPHETHRGLYSER
14   ASPILEPHEASNLYSASNMETARGALAHIS
15   ALALEUGLULYSGLYPHETHRILEASNGLU
16   TYRTHRILEARGPROLEUGLYVALTHRGLY
17   VALALAGLYGLUPROLEUPROVALASPSER
18   GLUGLNASPILEPHEASPTYRILEGLNTRP
19   ARGTYRARGGLUPROLYSASPARGSERGLU

Entity 2, XRCC1-NTD 157 residues - 17358 Da.

1   METPROGLUILEARGLEUARGHISVALVAL
2   SERCYSSERSERGLNASPSERTHRHISCYS
3   ALAGLUASNLEULEULYSALAASPTHRTYR
4   ARGLYSTRPARGALAALALYSALAGLYGLU
5   LYSTHRILESERVALVALLEUGLNLEUGLU
6   LYSGLUGLUGLNILEHISSERVALASPILE
7   GLYASNASPGLYSERALAPHEVALGLUVAL
8   LEUVALGLYSERSERALAGLYGLYALAGLY
9   GLUGLNASPTYRGLUVALLEULEUVALTHR
10   SERSERPHEMETSERPROSERGLUSERARG
11   SERGLYSERASNPROASNARGVALARGMET
12   PHEGLYPROASPLYSLEUVALARGALAALA
13   ALAGLULYSARGTRPASPARGVALLYSILE
14   VALCYSSERGLNPROTYRSERLYSASPSER
15   PROPHEGLYLEUSERPHEVALARGPHEHIS
16   SERPROPROASPLYSASPGLU

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:

NameSampleSample stateSample conditions
2D TROSY 1H-15N HSQCnot availablenot availablenot available
2D 1H-15N HSQCnot availablenot availablenot available
2D CT 1H-13C HSQCnot availablenot availablenot available
3D TROSY HNCACBnot availablenot availablenot available
3D TROSY HNCOnot availablenot availablenot available
3D (HM)CMC(CM)HMnot availablenot availablenot available
3D 15N,13C NOESYnot availablenot availablenot 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 shifts
SPARKY: Backbone or all simulated shifts