BMRB Entry 18823

Name: 1H, 13C and 15N resonance assignments of the C-terminal domain of PpdD
Published: 2013-01-29

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PDB ID: 6gms
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR18823
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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:

1H, 13C and 15N resonance assignments of the C-terminal domain of PpdD

Deposition date:

2012-11-06

Original release date:

2013-01-29

Authors:

Amorim, Gisele; Cisneros, David; Delepierre, Muriel; Francetic, Olivera; Izadi-Pruneyre, Nadia

Citation:

Citation: Amorim, Gisele; Cisneros, David; Delepierre, Muriel; Francetic, Olivera; Izadi-Pruneyre, Nadia. "(1)H, (15)N and (13)C resonance assignments of PpdD, a type IV pilin from enterohemorrhagic Escherichia coli." Biomol. NMR Assignments ., .-. (2012).
PubMed: 23242787

Assembly members:

Assembly members:
PpdD, polymer, 132 residues, 14227.7895 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: pET22b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
PpdD: MENYLRKAALTDMLQTFVPY RTAVELCALEHGGLDTCDGG SNGIPSPTTTRYVSAMSVAK GVVSLTGQESLNGLSVVMTP GWDNANGVTGWARNCNIQSD SALQQACEDVFRFDDANLVP RGSGLEHHHHHH

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	460
15N chemical shifts	124
1H chemical shifts	759

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	prepilin peptidase-dependent protein D	1

Entities:

Entity 1, prepilin peptidase-dependent protein D 132 residues - 14227.7895 Da.

1

MET

GLU

ASN

TYR

LEU

ARG

LYS

ALA

LEU

2

THR

ASP

MET

LEU

GLN

THR

PHE

VAL

PRO

TYR

3

ARG

THR

ALA

VAL

GLU

LEU

CYS

ALA

LEU

GLU

4

HIS

GLY

LEU

ASP

THR

CYS

ASP

GLY

5

SER

ASN

GLY

ILE

PRO

SER

PRO

THR

6

ARG

TYR

VAL

SER

ALA

MET

SER

VAL

ALA

LYS

7

GLY

VAL

SER

LEU

THR

GLY

GLN

GLU

SER

8

LEU

ASN

GLY

LEU

SER

VAL

MET

THR

PRO

9

GLY

TRP

ASP

ASN

ALA

ASN

GLY

VAL

THR

GLY

10

TRP

ALA

ARG

ASN

CYS

ASN

ILE

GLN

SER

ASP

11

SER

ALA

LEU

GLN

ALA

CYS

GLU

ASP

VAL

12

PHE

ARG

PHE

ASP

ALA

ASN

LEU

VAL

PRO

13

ARG

GLY

SER

GLY

LEU

GLU

HIS

14

HIS

Samples:

sample_1: PpdD, [U-13C; U-15N], 0.9 mM; sodium phosphate 50 mM; sodium chloride 50 mM; D2O 15%

sample_conditions_1: ionic strength: 0.1 M; pH: 7; 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	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1

Software:

CcpNnmr_Analysis v2.1, CCPN - chemical shift assignment, data analysis, peak picking

NMR spectrometers:

Varian INOVA 600 MHz

DBJ	BAB33535 BAB96678 BAG75632 BAI23471 BAI34110
EMBL	CAQ30623 CAR01475 CAR06329 CAR11328 CAR16249
GB	AAC36923 AAC73219 AAG54412 AAN41769 AAP15650
REF	NP_308139 NP_414650 NP_706062 WP_000360887 WP_000360895
SP	P36647
AlphaFold	P36647