BMRB Entry 5625

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PDB ID: 1a2i
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR5625
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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:

Sequential assignment of the ferricytochrome c3 from Desulfovibrio vulgaris Hildenborough

Deposition date:

2002-12-16

Original release date:

2007-11-05

Authors:

Messias, Ana; Aguiar, Antonio; Turner, David; Xavier, Antonio

Citation:

Citation: Messiasa, Ana; Aguiara, Antonio; Brennana, Lorraine; Salgueiroa, Carlos; Saraivaa, Ligia; Xaviera, Antonio; Turner, David. "Solution structures of tetrahaem ferricytochrome c3 from Desulfovibrio vulgaris (Hildenborough) and its K45Q mutant: The molecular basis of cooperativity" Biochim. Biophys. Acta. 1757, 143-153 (2006).
PubMed: 16527248

Assembly members:

Assembly members:
cytochrome c3, polymer, 107 residues, 14000 Da.
HEC, non-polymer, 618.503 Da.

Natural source:

Natural source: Common Name: Desulfovibrio vulgaris Hildenborough Taxonomy ID: 881 Superkingdom: Bacteria Kingdom: not available Genus/species: Desulfovibrio vulgaris

Experimental source:

Experimental source: Production method: purified from the natural source

Entity Sequences (FASTA):

Entity Sequences (FASTA):
cytochrome c3: APKAPADGLKMEATKQPVVF NHSTHKSVKCGDCHHPVNGK EDYRKCGTAGCHDSMDKKDK SAKGYYHVMHDKNTKFKSCV GCHVEVAGADAAKKKDLTGC KKSKCHE

Data sets:

assigned_chemical_shifts

Data type	Count
1H chemical shifts	742

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	cytochrome c3	1
2	heme, I	2
3	heme, II	2
4	heme, III	2
5	heme, IV	2

Entities:

Entity 1, cytochrome c3 107 residues - 14000 Da.

1

ALA

PRO

LYS

ALA

PRO

ALA

ASP

GLY

LEU

LYS

2

MET

GLU

ALA

THR

LYS

GLN

PRO

VAL

PHE

3

ASN

HIS

SER

THR

HIS

LYS

SER

VAL

LYS

CYS

4

GLY

ASP

CYS

HIS

PRO

VAL

ASN

GLY

LYS

5

GLU

ASP

TYR

ARG

LYS

CYS

GLY

THR

ALA

GLY

6

CYS

HIS

ASP

SER

MET

ASP

LYS

ASP

LYS

7

SER

ALA

LYS

GLY

TYR

HIS

VAL

MET

HIS

8

ASP

LYS

ASN

THR

LYS

PHE

LYS

SER

CYS

VAL

9

GLY

CYS

HIS

VAL

GLU

VAL

ALA

GLY

ALA

ASP

10

ALA

LYS

ASP

LEU

THR

GLY

CYS

11

LYS

SER

LYS

CYS

HIS

GLU

Entity 2, heme, I - C34 H34 Fe N4 O4 - 618.503 Da.

1

HEC

Samples:

sample_1: cytochrome c3 2.7 mM; ampicillin 127 uM; kanamicin 78 uM; chloramphenicol 141 uM; H2O 92%; D2O 8%

sample_2: cytochrome c3 2.7 mM; ampicillin 127 uM; kanamicin 78 uM; chloramphenicol 141 uM; D2O 100%

conditions_1: pH*: 7.1; temperature: 303 K

conditions_2: pH*: 7.1; temperature: 303 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D-1H-NOESY	not available	not available	not available
2D-1H-TOCSY	not available	not available	not available
2D-1H-COSY	not available	not available	not available

Software:

XEASY -

NMR spectrometers:

BRUKER DRX 500 MHz

BMRB	4291 5239 6634
PDB	1A2I 1GX7 1MDV 2BPN 2CTH 2CYM
EMBL	CAA27847
GB	AAS97641 ABM27239 ADP88070
REF	WP_010940429 YP_005703708 YP_012381 YP_965666
SP	P00131
AlphaFold	P00131 P00131 P00131