BMRB Entry 5333

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PDB ID: 1it1
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR5333
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:

Redox-Coupled Conformational Alternations in Cytochrome c3 from D. vulgaris Miyazaki F on the Basis of its Reduced Solution Structure

Deposition date:

2002-03-26

Original release date:

2002-06-13

Authors:

Harada, Erisa; Fukuoka, Yuki; Ohmura, Tomoaki; Fukunishi, Arima; Kawai, Gota; Fujiwara, Toshimichi; Akutsu, Hideo

Citation:

Citation: Harada, Erisa; Fukuoka, Yuki; Ohmura, Tomoaki; Fukunishi, Arima; Kawai, Gota; Fujiwara, Toshimichi; Akutsu, Hideo. "Redox-coupled Conformational Alternations in Cytochrome c3 from D. vulgaris Miyazaki F on the Basis of its Reduced Solution Structure" J. Mol. Biol. 319, 767-778 (2002).
PubMed: 12054869

Assembly members:

Assembly members:
cytochrome c3, polymer, 107 residues, Formula weight is not available
HEM, non-polymer, 616.487 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: 883 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: APKAPADGLKMDKTKQPVVF NHSTHKAVKCGDCHHPVNGK EDYQKCATAGCHDNMDKKDK SAKGYYHAMHDKGTKFKSCV GCHLETAGADAAKKKELTGC KGSKCHS

Data sets:

assigned_chemical_shifts

Data type	Count
1H chemical shifts	782
15N chemical shifts	115

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	cytochrome c3 peptide	1
2	heme 1	2
3	heme 2	2
4	heme 3	2
5	heme 4	2

Entities:

Entity 1, cytochrome c3 peptide 107 residues - Formula weight is not available

1

ALA

PRO

LYS

ALA

PRO

ALA

ASP

GLY

LEU

LYS

2

MET

ASP

LYS

THR

LYS

GLN

PRO

VAL

PHE

3

ASN

HIS

SER

THR

HIS

LYS

ALA

VAL

LYS

CYS

4

GLY

ASP

CYS

HIS

PRO

VAL

ASN

GLY

LYS

5

GLU

ASP

TYR

GLN

LYS

CYS

ALA

THR

ALA

GLY

6

CYS

HIS

ASP

ASN

MET

ASP

LYS

ASP

LYS

7

SER

ALA

LYS

GLY

TYR

HIS

ALA

MET

HIS

8

ASP

LYS

GLY

THR

LYS

PHE

LYS

SER

CYS

VAL

9

GLY

CYS

HIS

LEU

GLU

THR

ALA

GLY

ALA

ASP

10

ALA

LYS

GLU

LEU

THR

GLY

CYS

11

LYS

GLY

SER

LYS

CYS

HIS

SER

Entity 2, heme 1 - C34 H32 Fe N4 O4 - 616.487 Da.

1

HEM

Samples:

sample: cytochrome c3, [U-15N], 1.0 – 2.0 mM

sample_conditon: pH: 7.0 na; temperature: 303 K

Experiments:

Name	Sample	Sample state	Sample conditions
1H-15N NOESY	sample	not available	sample_conditon
1H-15N TOCSY	sample	not available	sample_conditon
NOESY	sample	not available	sample_conditon
DQF-COSY	sample	not available	sample_conditon
E-COSY	sample	not available	sample_conditon

Software:

NMR-Pipe/Pipp v4.0 -

NMR spectrometers:

Bruker DRX 600 MHz
Bruker AMX 500 MHz
Bruker DRX 400 MHz

BMRB	6572
PDB	1IT1 1J0O 1J0P 1WR5 2CDV 2EWI 2EWK 2EWU 2FFN 2YXC 2YYW 2YYX 2Z47
DBJ	BAA06511
GB	ACL09439 EGY24874
PRF	0607221A 1916446A
REF	WP_007526318 WP_015946129 YP_002436907
SP	P00132
AlphaFold	P00132 P00132