BMRB Entry 50453

Name: DegP-PDZ1PDZ2-50C
Published: 2021-10-15

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR50453

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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:

DegP-PDZ1PDZ2-50C

Deposition date:

2020-09-02

Original release date:

2021-10-15

Authors:

Sulskis, Darius; Thoma, Johannes; Burmann, Bjorn

Citation:

Citation: Sulskis, Darius; Thoma, Johannes; Burmann, Bjorn. "Structural basis of DegP protease temperature-dependent activation" Sci. Adv. 7, eabj1816-eabj1816 (2021).
PubMed: 34878848

Assembly members:

Assembly members:
entity_1, polymer, 188 residues, 19610 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 Vector: pET28a(+)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: KRGELGIMGTELNSELAKAM KVDAQRGAFVSQVLPNSSAA KAGIKAGDVITSLNGKPISS FAALRAQVGTMPVGSKLTLG LLRDGKQVNVNLELQQSSQN QVDSSSIFNGIEGAEMSNKG KDQGVVVNNVKTGTPAAQIG LKKGDVIIGANQQAVKNIAE LRKVLDSKPSVLALNIQRGD STIYLLMQ

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	724
15N chemical shifts	146
1H chemical shifts	1180

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	PDZ1-PDZ2	1

Entities:

Entity 1, PDZ1-PDZ2 188 residues - 19610 Da.

PDZ1-PDZ2 domain (261-448 a.a.) of DegP

1

LYS

ARG

GLY

GLU

LEU

GLY

ILE

MET

GLY

THR

2

GLU

LEU

ASN

SER

GLU

LEU

ALA

LYS

ALA

MET

3

LYS

VAL

ASP

ALA

GLN

ARG

GLY

ALA

PHE

VAL

4

SER

GLN

VAL

LEU

PRO

ASN

SER

ALA

5

LYS

ALA

GLY

ILE

LYS

ALA

GLY

ASP

VAL

ILE

6

THR

SER

LEU

ASN

GLY

LYS

PRO

ILE

SER

7

PHE

ALA

LEU

ARG

ALA

GLN

VAL

GLY

THR

8

MET

PRO

VAL

GLY

SER

LYS

LEU

THR

LEU

GLY

9

LEU

ARG

ASP

GLY

LYS

GLN

VAL

ASN

VAL

10

ASN

LEU

GLU

LEU

GLN

SER

GLN

ASN

11

GLN

VAL

ASP

SER

ILE

PHE

ASN

GLY

12

ILE

GLU

GLY

ALA

GLU

MET

SER

ASN

LYS

GLY

13

LYS

ASP

GLN

GLY

VAL

ASN

VAL

14

LYS

THR

GLY

THR

PRO

ALA

GLN

ILE

GLY

15

LEU

LYS

GLY

ASP

VAL

ILE

GLY

ALA

16

ASN

GLN

ALA

VAL

LYS

ASN

ILE

ALA

GLU

17

LEU

ARG

LYS

VAL

LEU

ASP

SER

LYS

PRO

SER

18

VAL

LEU

ALA

LEU

ASN

ILE

GLN

ARG

GLY

ASP

19

SER

THR

ILE

TYR

LEU

MET

GLN

Samples:

sample_1: PDZ1-PDZ2 domains of DegP, [U-100% 13C; U-100% 15N], 450 uM; D2O, [U-100% 2H], 10%; H2O 90%; potassium phosphate 25 mM; EDTA 1 mM; TCEP 1 mM

sample_conditions_1: ionic strength: 25 mM; pH: 7.0; pressure: 1 atm; temperature: 323 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N TROSY	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	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 HN(CA)CO	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D H(CC)(CO)NH	sample_1	isotropic	sample_conditions_1
3D (H)CC(CO)NH	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1

Software:

TOPSPIN v3.5 - collection, data analysis

CARA v1.9.1.7 - chemical shift assignment, chemical shift calculation, data analysis, peak picking

qMDD v3.2 - processing

NMRPipe v9.6 - processing

NMR spectrometers:

Bruker AVANCE III 800 MHz
Bruker AVANCE III 700 MHz

UNP	P0C0V0
AlphaFold	P15724