BMRB Entry 34534

Name: Spor protein DedD
Published: 2020-11-06

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PDB ID: 6ztg
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34534
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:

Spor protein DedD

Deposition date:

2020-07-20

Original release date:

2020-11-06

Authors:

Pazos, M.; Peters, K.; Boes, A.; Safaei, Y.; Kenward, C.; Caveney, N.; Laguri, C.; Breukink, E.; Strynadka, N.; Simorre, J.; Terrak, M.; Vollmer, W.

Citation:

Citation: Pazos, Manuel; Peters, Katharina; Boes, Adrien; Safaei, Yalda; Kenward, Calem; Caveney, Nathanael; Laguri, Cedric; Breukink, Eefjan; Strynadka, Natalie; Simorre, Jean-Pierre; Terrak, Mohammed; Vollmer, Waldemar. "SPOR Proteins Are Required for Functionality of Class A Penicillin-Binding Proteins in Escherichia coli" mBio 11, e02796-20-e02796-20 (2020).
PubMed: 33144379

Assembly members:

Assembly members:
entity_1, polymer, 193 residues, 20158.920 Da.

Natural source:

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

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: DGQKKHYQDEFAAIPLVPKA GDRDEPDMMPAATQALPTQP PEGAAEEVRAGDAAAPSLDP ATIAANNTEFEPEPAPVAPP KPKPVEPPKPKVEAPPAPKP EPKPVVEEKAAPTGKAYVVQ LGALKNADKVNEIVGKLRGA GYRVYTSPSTPVQGKITRIL VGPDASKDKLKGSLGELKQL SGLSGVVMGYTPN

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	477
15N chemical shifts	150
1H chemical shifts	836

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_1 193 residues - 20158.920 Da.

1

ASP

GLY

GLN

LYS

HIS

TYR

GLN

ASP

GLU

2

PHE

ALA

ILE

PRO

LEU

VAL

PRO

LYS

ALA

3

GLY

ASP

ARG

ASP

GLU

PRO

ASP

MET

PRO

4

ALA

THR

GLN

ALA

LEU

PRO

THR

GLN

PRO

5

PRO

GLU

GLY

ALA

GLU

VAL

ARG

ALA

6

GLY

ASP

ALA

PRO

SER

LEU

ASP

PRO

7

ALA

THR

ILE

ALA

ASN

THR

GLU

PHE

8

GLU

PRO

GLU

PRO

ALA

PRO

VAL

ALA

PRO

9

LYS

PRO

LYS

PRO

VAL

GLU

PRO

LYS

PRO

10

LYS

VAL

GLU

ALA

PRO

ALA

PRO

LYS

PRO

11

GLU

PRO

LYS

PRO

VAL

GLU

LYS

ALA

12

ALA

PRO

THR

GLY

LYS

ALA

TYR

VAL

GLN

13

LEU

GLY

ALA

LEU

LYS

ASN

ALA

ASP

LYS

VAL

14

ASN

GLU

ILE

VAL

GLY

LYS

LEU

ARG

GLY

ALA

15

GLY

TYR

ARG

VAL

TYR

THR

SER

PRO

SER

THR

16

PRO

VAL

GLN

GLY

LYS

ILE

THR

ARG

ILE

LEU

17

VAL

GLY

PRO

ASP

ALA

SER

LYS

ASP

LYS

LEU

18

LYS

GLY

SER

LEU

GLY

GLU

LEU

LYS

GLN

LEU

19

SER

GLY

LEU

SER

GLY

VAL

MET

GLY

TYR

20

THR

PRO

ASN

Samples:

sample_1: DedD, [U-13C; U-15N], 1.08 mM

sample_conditions_1: ionic strength: 300 mM; pH: 7; pressure: 1 Pa; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1

Software:

CNS, Brunger A. T. et.al. - refinement

ARIA, Linge, O'Donoghue and Nilges - structure calculation

CcpNmr Analysis, CCPN - chemical shift assignment, peak picking

NMR spectrometers:

Bruker AVANCE III 950 MHz

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