BMRB Entry 25640

Name: STRUCTURE OF OXIDIZED HORSE HEART CYTOCHROME C ENCAPSULATED IN REVERSE MICELLES
Published: 2015-10-26

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PDB ID: 2n3b
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR25640
MolProbity Validation Chart

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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: STRUCTURE OF OXIDIZED HORSE HEART CYTOCHROME C ENCAPSULATED IN REVERSE MICELLES PubMed: 26487716

Deposition date: 2015-05-27 Original release date: 2015-10-26

Authors: O'Brien, Evan; Nucci, Nathaniel; Fuglestad, Brian; Tommos, Cecilia; Wand, A. Joshua

Citation: O'Brien, Evan; Nucci, Nathaniel; Fuglestad, Brian; Tommos, Cecilia; Wand, A. Joshua. "Defining the Apoptotic Trigger: THE INTERACTION OF CYTOCHROME c AND CARDIOLIPIN" J. Biol. Chem. 290, 30879-30887 (2015).

Assembly members:
entity_1, polymer, 105 residues, 11744.722 Da.
WATER, water, 18.015 Da.

Natural source: Common Name: odd-toed ungulates Taxonomy ID: 9796 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Equus caballus

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

Entity Sequences (FASTA):
entity_1: GDVEKGKKIFVQKCAQCXTV EKGGKHKTGPNLHGLFGRKT GQAPGFTYTDANKNKGITWK EETLMEYLENPKKYIPGTKM IFAGIKKKTEREDLIAYLKK ATNEX

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	396
15N chemical shifts	103
1H chemical shifts	697

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1
2	water	2

Entities:

Entity 1, entity_1 105 residues - 11744.722 Da.

Normal histidines are found at residues 26 and 33, while NE2 deprotonated histidine is present at residue 18 in order to coordinate the heme residue (HEC 105). Four waters (residues 200-203) are also present in the structure.

1

GLY

ASP

VAL

GLU

LYS

GLY

LYS

ILE

PHE

2

VAL

GLN

LYS

CYS

ALA

GLN

CYS

HSD

THR

VAL

3

GLU

LYS

GLY

LYS

HIS

LYS

THR

GLY

PRO

4

ASN

LEU

HIS

GLY

LEU

PHE

GLY

ARG

LYS

THR

5

GLY

GLN

ALA

PRO

GLY

PHE

THR

TYR

THR

ASP

6

ALA

ASN

LYS

ASN

LYS

GLY

ILE

THR

TRP

LYS

7

GLU

THR

LEU

MET

GLU

TYR

LEU

GLU

ASN

8

PRO

LYS

TYR

ILE

PRO

GLY

THR

LYS

MET

9

ILE

PHE

ALA

GLY

ILE

LYS

THR

GLU

10

ARG

GLU

ASP

LEU

ILE

ALA

TYR

LEU

LYS

11

ALA

THR

ASN

GLU

HEC

Entity 2, water - 18.015 Da.

1

HOH

Samples:

sample_1: entity_1, [U-100% 13C; U-100% 15N], 0.15 mM; H2O 1.5 M; sodium phosphate 25 mM; 1-decanoyl-rac-glycerol 105 mM; lauryldimethylamine-N-oxide 45 mM; hexanol 8 mM; pentane, [U-99% 2H], 8.67 M

sample_2: entity_1, [U-100% 15N], 0.15 mM; H2O 1.5 M; sodium phosphate 25 mM; 1-decanoyl-rac-glycerol 105 mM; lauryldimethylamine-N-oxide 45 mM; hexanol 8 mM; pentane, [U-99% 2H], 8.67 M

sample_conditions_1: pH: 7.4; 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 HNCA	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D H(CCO)NH	sample_1	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
4D 1H-15N-13C-1H NOESY	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_1

Software:

Felix, Accelrys Software Inc. - processing

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

SPARKY, Goddard - data analysis, peak picking

TOPSPIN, Bruker Biospin - collection

X-PLOR_NIH, Schwieters, Kuszewski, Tjandra and Clore - structure solution

TALOS, Cornilescu, Delaglio and Bax - data analysis

NMR spectrometers:

Bruker Avance 500 MHz

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts