BMRB Entry 11590

Name: Solution Structure of the PhoP DNA-Binding Domain from Mycobacterium tuberculosis
Published: 2015-08-10

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PDB ID: 2rv8
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR11590
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution Structure of the PhoP DNA-Binding Domain from Mycobacterium tuberculosis

Deposition date:

2015-04-17

Original release date:

2015-08-10

Authors:

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

Citation:

Citation: Macdonald, Ramsay; Sarkar, Dibyendu; Amer, Brendan; Clubb, Robert. "Solution structure of the PhoP DNA-binding domain from Mycobacterium tuberculosis" J. Biomol. NMR ., .-. (2015).
PubMed: 26209027

Assembly members:

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

Natural source:

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

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET-15b

Entity Sequences (FASTA):

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

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	453
15N chemical shifts	98
1H chemical shifts	673

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	PhoP DNA-Binding Domain	1

Entities:

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

Residues 120-141 represent a histidine-tag

1

MET

GLY

SER

HIS

2

SER

GLY

LEU

VAL

PRO

ARG

GLY

SER

HIS

3

MET

LYS

GLY

ASN

LYS

GLU

PRO

ARG

ASN

VAL

4

ARG

LEU

THR

PHE

ALA

ASP

ILE

GLU

LEU

ASP

5

GLU

THR

HIS

GLU

VAL

TRP

LYS

ALA

GLY

6

GLN

PRO

VAL

SER

LEU

SER

PRO

THR

GLU

PHE

7

THR

LEU

ARG

TYR

PHE

VAL

ILE

ASN

ALA

8

GLY

THR

VAL

LEU

SER

LYS

PRO

LYS

ILE

LEU

9

ASP

HIS

VAL

TRP

ARG

TYR

ASP

PHE

GLY

10

ASP

VAL

ASN

VAL

GLU

SER

TYR

VAL

SER

11

TYR

LEU

ARG

LYS

ILE

ASP

THR

GLY

GLU

12

LYS

ARG

LEU

HIS

THR

LEU

ARG

GLY

VAL

13

GLY

TYR

VAL

LEU

ARG

GLU

PRO

ARG

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:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_2	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNHA	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-15N TOCSY	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_2	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_2	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-COSY	sample_2	isotropic	sample_conditions_1
3D HN(CA)CO	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D HBHANH	sample_1	isotropic	sample_conditions_1
3D (H)CCH-TOCSY	sample_2	isotropic	sample_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

PDB	2RV8 3R0J
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