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 11590

Title: Solution Structure of the PhoP DNA-Binding Domain from Mycobacterium tuberculosis   PubMed: 26209027

Authors: Macdonald, Ramsay; Sarkar, Dibyendu; Amer, Brendan; Clubb, Robert

Citation: Macdonald, Ramsay; Sarkar, Dibyendu; Amer, Brendan; Clubb, Robert. "Solution structure of the PhoP DNA-binding domain from Mycobacterium tuberculosis"  J. Biomol. NMR ., .-. (2015).

Assembly members:
PhoPC, polymer, 128 residues, 14723.858 Da.

Natural source:   Common Name: Mycobacterium tuberculosis   Taxonomy ID: 1773   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Mycobacterium tuberculosis

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

Entity Sequences (FASTA):
PhoPC: MGSSHHHHHHSSGLVPRGSH MKGNKEPRNVRLTFADIELD EETHEVWKAGQPVSLSPTEF TLLRYFVINAGTVLSKPKIL DHVWRYDFGGDVNVVESYVS YLRRKIDTGEKRLLHTLRGV GYVLREPR

Data sets:
Data typeCount
13C chemical shifts453
15N chemical shifts98
1H chemical shifts673

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1PhoP DNA-Binding Domain1

Entities:

Entity 1, PhoP DNA-Binding Domain 128 residues - 14723.858 Da.

Residues 120-141 represent a histidine-tag

1   METGLYSERSERHISHISHISHISHISHIS
2   SERSERGLYLEUVALPROARGGLYSERHIS
3   METLYSGLYASNLYSGLUPROARGASNVAL
4   ARGLEUTHRPHEALAASPILEGLULEUASP
5   GLUGLUTHRHISGLUVALTRPLYSALAGLY
6   GLNPROVALSERLEUSERPROTHRGLUPHE
7   THRLEULEUARGTYRPHEVALILEASNALA
8   GLYTHRVALLEUSERLYSPROLYSILELEU
9   ASPHISVALTRPARGTYRASPPHEGLYGLY
10   ASPVALASNVALVALGLUSERTYRVALSER
11   TYRLEUARGARGLYSILEASPTHRGLYGLU
12   LYSARGLEULEUHISTHRLEUARGGLYVAL
13   GLYTYRVALLEUARGGLUPROARG

Samples:

sample_1: sodium phosphate 50.0 mM; sodium chloride 300.0 mM; sodium azide 0.01%; PhoPC, [U-100% 13C; U-100% 15N], 1.0 ± 0.5 mM; H2O 93%; D2O, [U-2H], 7%

sample_2: sodium phosphate 50.0 mM; sodium chloride 300.0 mM; sodium azide 0.01%; PhoPC, [U-100% 13C; U-100% 15N], 1.0 ± 0.5 mM; D2O, [U-2H], 100%

sample_conditions_1: ionic strength: 350 mM; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_2isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_2isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D HNHAsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-15N TOCSYsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_2isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_2isotropicsample_conditions_1
3D HCCH-TOCSYsample_2isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D HCCH-COSYsample_2isotropicsample_conditions_1
3D HN(CA)COsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
3D HBHANHsample_1isotropicsample_conditions_1
3D (H)CCH-TOCSYsample_2isotropicsample_conditions_1

Software:

X-PLOR_NIH v2.25, Schwieters, Kuszewski, Tjandra and Clore - refinement

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

NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

PIPP, Garrett - peak picking

TALOS, Cornilescu, Delaglio and Bax - dihedral angle calculation

ProcheckNMR, Laskowski and MacArthur - statistics

UNIO, Herrmann - data analysis, peak picking, structure solution

ATNOS-CANDID, Herrmann, Guntert and Wuthrich - data analysis, peak picking

CARA, Keller and Wuthrich - chemical shift assignment

NMR spectrometers:

  • Bruker Avence 500 MHz
  • Bruker Avence 600 MHz
  • Bruker Avence 800 MHz

Related Database Links:

PDB
DBJ BAH25072 BAL64650 BAQ04662 GAA44527
EMBL CAL70795 CCC25841 CCC43101 CCC63367 CCE36300
GB AAK45023 ABQ72495 ABR05115 ACT23809 AEB02905
REF NP_215271 NP_854438 WP_003403867 WP_003915456 WP_012054162