BMRB Entry 34552

Name: Structure-function analyses of dual-BON domain protein DolP identifies phospholipid binding as a new mechanism for protein localisation to the cell division site
Published: 2020-12-26

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PDB ID: 7a2d
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34552
MolProbity Validation Chart

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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:

Structure-function analyses of dual-BON domain protein DolP identifies phospholipid binding as a new mechanism for protein localisation to the cell division site

Deposition date:

2020-08-17

Original release date:

2020-12-26

Authors:

Morris, F.; Knowles, T.; Maderbocus, R.; Jeeves, M.; Kirwan, J.; Heinz, E.; Wells, T.; Browning, D.; Sevastsyanovich, Y.; Leyton, D.; Rossiter, A.; Bavro, V.; Sridhar, P.; Ward, D.; Shimwell, N.; Martin, A.; Sahl, J.; Wardius, C.; Walker, D.; Lithgow, T.; Viant, M.; Rasko, D.; Cunningham, A.; Overduin, M.; Henderson, I.

Citation:

Citation: Bryant, Jack Alfred; Morris, Faye; Knowles, Timothy; Maderbocus, Riyaz; Heinz, Eva; Boelter, Gabriela; Alodaini, Dema; Colyer, Adam; Wotherspoon, Peter; Staunton, Kara; Jeeves, Mark; Browning, Douglas; Sevastsyanovich, Yanina; Wells, Timothy; Rossiter, Amanda; Bavro, Vassiliy; Sridhar, Pooja; Ward, Douglas; Chong, Zhi-Soon; Goodall, Emily Ca; Icke, Christopher; Teo, Alvin Ck; Chng, Shu-Sin; Roper, David; Lithgow, Trevor; Cunningham, Adam; Banzhaf, Manuel; Overduin, Michael; Henderson, Ian. "Structure of dual BON-domain protein DolP identifies phospholipid binding as a new mechanism for protein localisation" Elife 9, .-. (2020).
PubMed: 33315009

Assembly members:

Assembly members:
entity_1, polymer, 182 residues, 19324.738 Da.

Natural source:

Natural source: Common Name: E. coli Taxonomy ID: 1169330 Superkingdom: Bacteria Kingdom: not available Genus/species: Escherichia coli

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli BL21(DE3) Vector: PET26B

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: IAAAVVGTAAVGTKAATDPR SVGTQVDDGTLEVRVNSALS KDEQIKKEARINVTAYQGKV LLVGQSPNAELSARAKQIAM GVDGANEVYNEIRQGQPIGL GEASNDTWITTKVRSQLLTS DLVKSSNVKVTTENGEVFLM GLVTEREAKAAADIASRVSG VKRVTTAFTFIKGGLEHHHH HH

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list

Data type	Count
13C chemical shifts	686
15N chemical shifts	172
1H chemical shifts	1023

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1

Entities:

Entity 1, unit_1 182 residues - 19324.738 Da.

1

ILE

ALA

VAL

GLY

THR

ALA

2

VAL

GLY

THR

LYS

ALA

THR

ASP

PRO

ARG

3

SER

VAL

GLY

THR

GLN

VAL

ASP

GLY

THR

4

LEU

GLU

VAL

ARG

VAL

ASN

SER

ALA

LEU

SER

5

LYS

ASP

GLU

GLN

ILE

LYS

GLU

ALA

ARG

6

ILE

ASN

VAL

THR

ALA

TYR

GLN

GLY

LYS

VAL

7

LEU

VAL

GLY

GLN

SER

PRO

ASN

ALA

GLU

8

LEU

SER

ALA

ARG

ALA

LYS

GLN

ILE

ALA

MET

9

GLY

VAL

ASP

GLY

ALA

ASN

GLU

VAL

TYR

ASN

10

GLU

ILE

ARG

GLN

GLY

GLN

PRO

ILE

GLY

LEU

11

GLY

GLU

ALA

SER

ASN

ASP

THR

TRP

ILE

THR

12

THR

LYS

VAL

ARG

SER

GLN

LEU

THR

SER

13

ASP

LEU

VAL

LYS

SER

ASN

VAL

LYS

VAL

14

THR

GLU

ASN

GLY

GLU

VAL

PHE

LEU

MET

15

GLY

LEU

VAL

THR

GLU

ARG

GLU

ALA

LYS

ALA

16

ALA

ASP

ILE

ALA

SER

ARG

VAL

SER

GLY

17

VAL

LYS

ARG

VAL

THR

ALA

PHE

THR

PHE

18

ILE

LYS

GLY

LEU

GLU

HIS

19

HIS

Samples:

sample_1: DolP, [U-13C; U-15N], 1.5 mM; sodium phosphate 50 mM; NaN3 0.02 % w/v; sodium chloride 50 mM

sample_conditions_1: ionic strength: 0.05 M; pH: 6; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HN(CA)CO	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY-HSQC ALIPHATIC	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY-HSQC AROMATIC	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY-HSQC	sample_1	isotropic	sample_conditions_1
H(C)CONH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1

Software:

ARIA v2.3, LINGE - refinement

NMRFAM-SPARKY, Lee W, Tonelli M, Markley JL - chemical shift assignment, data analysis

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

PROCHECK / PROCHECK-NMR, Laskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thornton - refinement

CYANA v2.1, LASKOWSKI AND MACARTHUR (PROCHECKNMR) - refinement

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

TALOS, Cornilescu, Delaglio and Bax - data analysis

NMR spectrometers:

Varian INOVA 800 MHz

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