BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 17191

Title: Solution NMR Structure of a putative Uracil DNA glycosylase from Methanosarcina acetivorans, Northeast Structural Genomics Consortium Target MvR76

Authors: Aramini, James; Hamilton, Keith; Ciccosanti, Colleen; Wang, Huang; Lee, Hsiau-Wei; Rost, Burkhard; Acton, Thomas; Xiao, Rong; Everett, John; Montelione, Gaetano

Citation: Aramini, James; Hamilton, Keith; Ciccosanti, Colleen; Wang, Huang; Lee, Hsiau-Wei; Rost, Burkhard; Acton, Thomas; Xiao, Rong; Everett, John; Montelione, Gaetano. "Solution NMR Structure of a putative Uracil DNA glycosylase from Methanosarcina acetivorans, Northeast Structural Genomics Consortium Target MvR76"  To be published ., .-..

Assembly members:
MvR76, polymer, 166 residues, 18460.070 Da.

Natural source:   Common Name: Methanosarcina acetivorans   Taxonomy ID: 2214   Superkingdom: Archaea   Kingdom: not available   Genus/species: Methanosarcina acetivorans

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

Entity Sequences (FASTA):
MvR76: MIKRGFPAVLDENTEILILG SLPSDESIRKQQYYGNPGND FWRLVGHAIGENLQDMAYEK KLKTLKHNRIGLWDVFKAGS REGSQDSKIGDEEINDFSGL KEMVPKLRLICFNGRKAGEY EPLLRGMGYETKVLPSSSGA NRRFSKNRESEWEAVFRHLE HHHHHH

Data typeCount
13C chemical shifts712
15N chemical shifts170
1H chemical shifts1116
residual dipolar couplings210

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1MvR761

Entities:

Entity 1, MvR76 166 residues - 18460.070 Da.

C-terminal LEHHHHHH purification tag

1   METILELYSARGGLYPHEPROALAVALLEU
2   ASPGLUASNTHRGLUILELEUILELEUGLY
3   SERLEUPROSERASPGLUSERILEARGLYS
4   GLNGLNTYRTYRGLYASNPROGLYASNASP
5   PHETRPARGLEUVALGLYHISALAILEGLY
6   GLUASNLEUGLNASPMETALATYRGLULYS
7   LYSLEULYSTHRLEULYSHISASNARGILE
8   GLYLEUTRPASPVALPHELYSALAGLYSER
9   ARGGLUGLYSERGLNASPSERLYSILEGLY
10   ASPGLUGLUILEASNASPPHESERGLYLEU
11   LYSGLUMETVALPROLYSLEUARGLEUILE
12   CYSPHEASNGLYARGLYSALAGLYGLUTYR
13   GLUPROLEULEUARGGLYMETGLYTYRGLU
14   THRLYSVALLEUPROSERSERSERGLYALA
15   ASNARGARGPHESERLYSASNARGGLUSER
16   GLUTRPGLUALAVALPHEARGHISLEUGLU
17   HISHISHISHISHISHIS

Samples:

sample_1: MvR76, [U-100% 13C; U-100% 15N], 0.94 mM; MES 20 mM; sodium chloride 100 mM; calcium chloride 5 mM; DTT 10 mM; sodium azide 0.02%; DSS 50 uM; H2O 90%; D2O 10%

sample_2: MvR76, [U-5% 13C; U-100% 15N], 1.15 mM; MES 20 mM; sodium chloride 100 mM; calcium chloride 5 mM; DTT 10 mM; sodium azide 0.02%; DSS 50 uM; H2O 90%; D2O 10%

sample_3: MvR76, [U-5% 13C; U-100% 15N], 0.80 mM; MES 20 mM; sodium chloride 100 mM; calcium chloride 5 mM; DTT 10 mM; sodium azide 0.02%; DSS 50 uM; C12E5 PEG 4%; H2O 90%; D2O 10%

sample_4: MvR76, [U-5% 13C; U-100% 15N], 1.15 mM; MES 20 mM; sodium chloride 100 mM; calcium chloride 5 mM; DTT 10 mM; sodium azide 0.02%; DSS 50 uM; Polyacrylamide gel 7%; H2O 90%; D2O 10%

sample_conditions_1: pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1
2D 1H-13C HSQC high resolution (L/V methyl stereoassignment)sample_2isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HN(CA)COsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D CCH-TOCSYsample_1isotropicsample_conditions_1
3D HCCH-COSYsample_1isotropicsample_conditions_1
3D HNHAsample_1isotropicsample_conditions_1
3D HBHANHsample_1isotropicsample_conditions_1
1D 15N T1 and T2sample_1isotropicsample_conditions_1
2D 1H-15N hetNOEsample_1isotropicsample_conditions_1
NH J-modulationsample_3anisotropicsample_conditions_1
NH J-modulationsample_4anisotropicsample_conditions_1

Software:

CNS v1.1, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

CYANA v3.0, Guntert, Mumenthaler and Wuthrich - refinement, structure solution

AutoStruct v2.2.1, Huang, Tejero, Powers and Montelione - RPF analysis

PSVS v1.4, Bhattacharya and Montelione - structure quality analysis

NMRPipe v2.3, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

MolProbity v3.18, Richardson - structure quality analysis

TOPSPIN v2.1, Bruker Biospin - collection, data analysis

PDBStat v5.1, Tejero & Montelione - PDB coordinate analysis

PINE v1.0, Bahrami, Markley, Assadi, and Eghbalnia - chemical shift assignment

SPARKY v3.112, Goddard - data analysis, peak picking

TALOS+, Shen, Cornilescu, Delaglio and Bax - geometry optimization

PALES, PALES (Zweckstetter, Bax) - RDC analysis

VNMRJ v2.1, Varian - collection, data analysis

NMR spectrometers:

  • Bruker Avance 800 MHz
  • Bruker Avance 600 MHz
  • Varian INOVA 600 MHz

Related Database Links:

PDB
GB AAM03908
REF WP_011020513