BMRB Entry 11549

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR11549
MolProbity Validation Chart

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Title:
DnaT C-terminal domain
Deposition date:
2014-01-28
Original release date:
2014-10-06
Authors:
Abe, Yoshito; Tani, Junya; Fujiyama, Saki; Urabe, Masashi; Sato, Kenji; Aramaki, Takahiko; Katayama, Tsutomu; Ueda, Tadashi
Citation:

Citation: Fujiyama, Saki; Abe, Yoshito; Tani, Junya; Urabe, Masashi; Sato, Kenji; Aramaki, Takahiko; Katayama, Tsutomu; Ueda, Tadashi. "Structure and a novel mechanism of the primosome protein DnaT: formation of DnaT-ssDNA complex and dissociation of ssDNA from PriB-ssDNA complex."  J. Biol. Chem. ., .-..

Assembly members:

Assembly members:
DnaT, polymer, 98 residues, 10408.844 Da.

Natural source:

Natural source:   Common Name: E.. coli   Taxonomy ID: 562   Superkingdom: Eubacteria   Kingdom: not available   Genus/species: Escherichia coli

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET22b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
DnaT: MFAMYPDWQPDADFIRLAAL WGVALREPVTTEELASFIAY WQAEGKVFHHVQWQQKLARS LQIGRASNGGLPKRDVNTVS EPDSQIPPGFRGHHHHHH

Data sets:
Data typeCount
13C chemical shifts397
15N chemical shifts93
1H chemical shifts633

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1DnaT1

Entities:

Entity 1, DnaT 98 residues - 10408.844 Da.

First methionine is a initial codon for expression in Escherichia coli. Last 6 residues is affinity tag. This is the C-terminal domain of replication restart factor, DnaT

1   METPHEALAMETTYRPROASPTRPGLNPRO
2   ASPALAASPPHEILEARGLEUALAALALEU
3   TRPGLYVALALALEUARGGLUPROVALTHR
4   THRGLUGLULEUALASERPHEILEALATYR
5   TRPGLNALAGLUGLYLYSVALPHEHISHIS
6   VALGLNTRPGLNGLNLYSLEUALAARGSER
7   LEUGLNILEGLYARGALASERASNGLYGLY
8   LEUPROLYSARGASPVALASNTHRVALSER
9   GLUPROASPSERGLNILEPROPROGLYPHE
10   ARGGLYHISHISHISHISHISHIS

Samples:

sample_1: DnaT, [U-99% 13C; U-99% 15N], 0.5 mM; HEPES 20 mM; H2O 90%; D2O 10%

sample_2: DnaT, [U-99% 15N], 0.1 mM; HEPES 20 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 0 M; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D HCCH-COSYsample_1isotropicsample_conditions_1

Software:

CNS, Brunger A. T. et.al. - refinement

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution

TALOS, Cornilescu, Delaglio and Bax - prediction of torsion angle

NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - chemical shift assignment

olivia, olivia developer team - chemical shift assignment

NMR spectrometers:

  • Varian Unity 600 MHz

Related Database Links:

PDB
DBJ BAB38745 BAE78352 BAG80162 BAI28689 BAI33823
EMBL CAP78850 CAQ34722 CAR01325 CAR06127 CAR16096
GB AAA23699 AAA97261 AAC77318 AAG59545 AAN45808
REF NP_313349 NP_418782 NP_710101 WP_000098809 WP_000098810
SP A1AJN5 A7ZVQ2 A8A891 B1IS56 B1LEG6
AlphaFold A1AJN5 A7ZVQ2 A8A891 B1IS56 B1LEG6

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks