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Biological Magnetic Resonance Data Bank


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BMRB Entry 17783

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR17783
MolProbity Validation Chart

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Title: Solution Structure of the SPOR domain from E. coli DamX   PubMed: 23290046

Deposition date: 2011-07-15 Original release date: 2012-07-17

Authors: Williams, Kyle; Arends, S.J.; Popham, David; Fowler, C.; Weiss, David

Citation: Williams, Kyle; Yahashiri, Atsushi; Arends, S.J.; Popham, David; Fowler, C.; Weiss, David. "Nuclear Magnetic Resonance Solution Structure of the Peptidoglycan-Binding SPOR Domain from Escherichia coli DamX: Insights into Septal Localization"  Biochemistry 52, 627-639 (2013).

Assembly members:
DamX_SPOR_domain_polypeptide, polymer, 106 residues, 11876.272 Da.

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

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

Entity Sequences (FASTA):
DamX_SPOR_domain_polypeptide: MRGSHHHHHHGSNNNGSLKS APSSHYTLQLSSSSNYDNLN GWAKKENLKNYVVYETTRNG QPWYVLVSGVYASKEEAKKA VSTLPADVQAKNPWAKPLRQ VQADLK

Data sets:
Data typeCount
13C chemical shifts458
15N chemical shifts114
1H chemical shifts994
heteronuclear NOE values94
T1 relaxation values94
T2 relaxation values94

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1DamX SPOR domain1

Entities:

Entity 1, DamX SPOR domain 106 residues - 11876.272 Da.

first residue number is 323 residues 323-337 constitute an added affinity tag and linker the actual SPOR domain starts at residue 344

1   METARGGLYSERHISHISHISHISHISHIS
2   GLYSERASNASNASNGLYSERLEULYSSER
3   ALAPROSERSERHISTYRTHRLEUGLNLEU
4   SERSERSERSERASNTYRASPASNLEUASN
5   GLYTRPALALYSLYSGLUASNLEULYSASN
6   TYRVALVALTYRGLUTHRTHRARGASNGLY
7   GLNPROTRPTYRVALLEUVALSERGLYVAL
8   TYRALASERLYSGLUGLUALALYSLYSALA
9   VALSERTHRLEUPROALAASPVALGLNALA
10   LYSASNPROTRPALALYSPROLEUARGGLN
11   VALGLNALAASPLEULYS

Samples:

15N_DamX: DamX SPOR domain polypeptide, [U-99% 15N], 0.7 mM; H2O 90%; D2O, [U-99% 2H], 10%; potassium phosphate 50 mM; potassium chloride 50 mM

13C-15N_DamX_in_D2O: DamX SPOR domain polypeptide, [U-99% 13C; U-99% 15N], 0.7 mM; D2O, [U-99% 2H], 100%; potassium phosphate 50 mM; potassium chloride 50 mM

13C-15N_DamX: DamX SPOR domain polypeptide, [U-99% 13C; U-99% 15N], 0.7 mM; H2O 90%; D2O, [U-99% 2H], 10%; potassium phosphate 50 mM; potassium chloride 50 mM

15N_DamX_aligned: DamX SPOR domain polypeptide, [U-99% 15N], 0.7 mM; H2O 90%; D2O, [U-99% 2H], 10%; potassium phosphate 50 mM; potassium chloride 50 mM; PEG(C12E5):n-hexanol 5%

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

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQC15N_DamXisotropicsample_conditions_1
2D 1H-13C HMQC13C-15N_DamX_in_D2Oisotropicsample_conditions_1
3D HNCA13C-15N_DamXisotropicsample_conditions_1
3D HN(CO)CA13C-15N_DamXisotropicsample_conditions_1
3D HNCACB13C-15N_DamXisotropicsample_conditions_1
3D CBCA(CO)NH13C-15N_DamXisotropicsample_conditions_1
3D HNCO13C-15N_DamXisotropicsample_conditions_1
3D HN(CA)CO13C-15N_DamXisotropicsample_conditions_1
3D 1H-15N TOCSY15N_DamXisotropicsample_conditions_1
3D 1H-15N NOESY15N_DamXisotropicsample_conditions_1
2D DQF-COSY13C-15N_DamX_in_D2Oisotropicsample_conditions_1
2D 1H-1H NOESY13C-15N_DamX_in_D2Oisotropicsample_conditions_1
2D 1H-1H TOCSY13C-15N_DamX_in_D2Oisotropicsample_conditions_1
3D C(CO)NH13C-15N_DamXisotropicsample_conditions_1
3D H(CCO)NH13C-15N_DamXisotropicsample_conditions_1
(HB)CB(CGCD)HE13C-15N_DamX_in_D2Oisotropicsample_conditions_1
(HB)CB(CGCDCE)HE13C-15N_DamX_in_D2Oisotropicsample_conditions_1
3D 1H-13C NOESY13C-15N_DamX_in_D2Oisotropicsample_conditions_1
3D 1H-13C NOESY13C-15N_DamXisotropicsample_conditions_1
3D HCCH-TOCSY13C-15N_DamX_in_D2Oisotropicsample_conditions_1
2D 1H-15N IPAP HSQC15N_DamXisotropicsample_conditions_1
2D 1H-15N IPAP HSQC15N_DamX_alignedbicellesample_conditions_1
2D 15N T115N_DamXisotropicsample_conditions_1
2D 15N T215N_DamXisotropicsample_conditions_1
2D {1H}-15N NOE15N_DamXisotropicsample_conditions_1

Software:

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - peak picking, processing

VNMRJ v2.1B, Varian - collection

CCPN_Analysis v1.0.15, CCPN - chemical shift assignment, data analysis, peak picking

TALOS, Cornilescu, Delaglio and Bax - data analysis

CurveFit, Palmer - data analysis

X-PLOR NIH v2.23, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution

ProcheckNMR v3.5.4, Laskowski and MacArthur - structure analysis

NMR spectrometers:

  • Varian INOVA 600 MHz

Related Database Links:

PDB
DBJ BAB37653 BAE77903 BAG79173 BAI27646 BAI32816
EMBL CAA33253 CAP77835 CAQ33709 CAR00327 CAR04988
GB AAA58185 AAC76413 AAG58488 AAN44868 AAN82596
REF NP_312257 NP_417847 NP_709161 WP_000343127 WP_000343163
SP P11557 Q8X826

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