BMRB Entry 19985

Name: Backbone, side chain and heme resonance assignments of the triheme cytochrome PpcD from Geobacter sulfurreducens
Published: 2017-07-11

Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR19985

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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:

Backbone, side chain and heme resonance assignments of the triheme cytochrome PpcD from Geobacter sulfurreducens

Deposition date:

2014-05-22

Original release date:

2017-07-11

Authors:

Dantas, Joana; Salgueiro, Carlos; Bruix, Marta

Citation:

Citation: Dantas, Joana; Salgueiro, Carlos; Bruix, Marta. "Backbone, side chain and heme resonance assignments of the triheme cytochrome PpcD from Geobacter sulfurreducens" Biomol. NMR Assign. 9, 211-214 (2015).
PubMed: 25209145

Assembly members:

Assembly members:
PpcD_polypeptide, polymer, 72 residues, 7713.88 Da.
entity_HEM, non-polymer, 616.487 Da.

Natural source:

Natural source: Common Name: Geobacter sulfurreducens Taxonomy ID: 35554 Superkingdom: Bacteria Kingdom: not available Genus/species: Geobacter sulfurreducens

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pVA203

Entity Sequences (FASTA):

Entity Sequences (FASTA):
PpcD_polypeptide: HDKVVVLEAKNGNVTFDHKK HAGVKGECKACHETEAGGKI AGMGKDWAHKTCTGCHKEMG KGPTKCGECHKK

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	205
15N chemical shifts	78
1H chemical shifts	531

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	PpcD	1
2	PROTOPORPHYRIN IX CONTAINING FE_1	2
3	PROTOPORPHYRIN IX CONTAINING FE_2	2
4	PROTOPORPHYRIN IX CONTAINING FE_3	2

Entities:

Entity 1, PpcD 72 residues - 7713.88 Da.

1

HIS

ASP

LYS

VAL

LEU

GLU

ALA

LYS

2

ASN

GLY

ASN

VAL

THR

PHE

ASP

HIS

LYS

3

HIS

ALA

GLY

VAL

LYS

GLY

GLU

CYS

LYS

ALA

4

CYS

HIS

GLU

THR

GLU

ALA

GLY

LYS

ILE

5

ALA

GLY

MET

GLY

LYS

ASP

TRP

ALA

HIS

LYS

6

THR

CYS

THR

GLY

CYS

HIS

LYS

GLU

MET

GLY

7

LYS

GLY

PRO

THR

LYS

CYS

GLY

GLU

CYS

HIS

8

LYS

Entity 2, PROTOPORPHYRIN IX CONTAINING FE_1 - C34 H32 Fe N4 O4 - 616.487 Da.

1

HEM

Samples:

PpcD_unlabelled: PpcD polypeptide 2 mM; PROTOPORPHYRIN IX CONTAINING FE 6 mM; sodium phosphate 45 mM; sodium azide 0.04%

PpcD_15Nlabelled: PpcD polypeptide, [U-100% 15N], 2 mM; PROTOPORPHYRIN IX CONTAINING FE 6 mM; sodium phosphate 45 mM; sodium azide 0.04%

PpcD_13C15Nlabelled: PpcD polypeptide, [U-100% 13C; U-100% 15N], 2 mM; PROTOPORPHYRIN IX CONTAINING FE 6 mM; sodium phosphate 45 mM; sodium azide 0.04%

sample_condition_PpcD_unlabelled: ionic strength: 100 mM; pH: 7.1; pressure: 1 atm; temperature: 298 K

sample_condition_PpcD_13C15Nlabelled: ionic strength: 100 mM; pH: 7.1; pressure: 1 atm; temperature: 298 K

sample_condition_PpcD_15Nlabelled: ionic strength: 100 mM; pH: 7.1; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	PpcD_13C15Nlabelled	isotropic	sample_condition_PpcD_13C15Nlabelled
2D 1H-13C HSQC	PpcD_13C15Nlabelled	isotropic	sample_condition_PpcD_13C15Nlabelled
3D HNCA	PpcD_13C15Nlabelled	isotropic	sample_condition_PpcD_13C15Nlabelled
3D HNCACB	PpcD_13C15Nlabelled	isotropic	sample_condition_PpcD_13C15Nlabelled
3D HN(CO)CA	PpcD_13C15Nlabelled	isotropic	sample_condition_PpcD_13C15Nlabelled
3D CBCA(CO)NH	PpcD_13C15Nlabelled	isotropic	sample_condition_PpcD_13C15Nlabelled
3D HCCH-TOCSY	PpcD_13C15Nlabelled	isotropic	sample_condition_PpcD_13C15Nlabelled
3D HCCH-TOCSY	PpcD_13C15Nlabelled	isotropic	sample_condition_PpcD_13C15Nlabelled
2D 1H-1H COSY	PpcD_unlabelled	isotropic	sample_condition_PpcD_unlabelled
2D 1H-1H TOCSY	PpcD_unlabelled	isotropic	sample_condition_PpcD_unlabelled
2D 1H-1H NOESY	PpcD_unlabelled	isotropic	sample_condition_PpcD_unlabelled
3D 1H-15N TOCSY	PpcD_15Nlabelled	isotropic	sample_condition_PpcD_15Nlabelled
3D 1H-15N NOESY	PpcD_15Nlabelled	isotropic	sample_condition_PpcD_15Nlabelled

Software:

TOPSPIN, Bruker Biospin - collection, processing

SPARKY, Goddard - chemical shift assignment

NMR spectrometers:

Bruker Avance 800 MHz

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