BMRB Entry 15913

Name: Solution Structure of the IsdC NEAT domain bound to Zinc Protoporphyrin
Published: 2008-08-14

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PDB ID: 2k78
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR15913
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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:

Solution Structure of the IsdC NEAT domain bound to Zinc Protoporphyrin

Deposition date:

2008-08-07

Original release date:

2008-08-14

Authors:

Villareal, Valerie; Pilpa, Rosemarie; Robson, Scott; Fadeev, Evgeny; Clubb, Robert

Citation:

Citation: Villareal, Valerie; Pilpa, Rosemarie; Robson, Scott; Fadeev, Evgeny; Clubb, Robert. "The IsdC protein from Staphylococcus aureus uses a flexible binding pocket to capture heme" J. Biol. Chem. 283, 31591-31600 (2008).
PubMed: 18715872

Assembly members:

Assembly members:
IsdC, polymer, 147 residues, 14322.988 Da.
ZNH, non-polymer, 626.051 Da.

Natural source:

Natural source: Common Name: Staphylococcus aureus Taxonomy ID: 1280 Superkingdom: Bacteria Kingdom: not available Genus/species: Staphylococcus aureus

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET15b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
IsdC: MGSSHHHHHHSSGLVPRGSH MSANAADSGTLNYEVYKYNT NDTSIANDYFNKPAKYIKKN GKLYVQITVNHSHWITGMSI EGHKENIISKNTAKDERTSE FEVSKLNGKIDGKIDVYIDE KVNGKPFKYDHHYNITYKFN GPTDVAG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	488
15N chemical shifts	130
1H chemical shifts	730

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	IsdC	1
2	ZNH	2

Entities:

Entity 1, IsdC 147 residues - 14322.988 Da.

Residues 4-24 represent a Histidine-tag that was not included in the structure calculations

1

MET

GLY

SER

HIS

2

SER

GLY

LEU

VAL

PRO

ARG

GLY

SER

HIS

3

MET

SER

ALA

ASN

ALA

ASP

SER

GLY

THR

4

LEU

ASN

TYR

GLU

VAL

TYR

LYS

TYR

ASN

THR

5

ASN

ASP

THR

SER

ILE

ALA

ASN

ASP

TYR

PHE

6

ASN

LYS

PRO

ALA

LYS

TYR

ILE

LYS

ASN

7

GLY

LYS

LEU

TYR

VAL

GLN

ILE

THR

VAL

ASN

8

HIS

SER

HIS

TRP

ILE

THR

GLY

MET

SER

ILE

9

GLU

GLY

HIS

LYS

GLU

ASN

ILE

SER

LYS

10

ASN

THR

ALA

LYS

ASP

GLU

ARG

THR

SER

GLU

11

PHE

GLU

VAL

SER

LYS

LEU

ASN

GLY

LYS

ILE

12

ASP

GLY

LYS

ILE

ASP

VAL

TYR

ILE

ASP

GLU

13

LYS

VAL

ASN

GLY

LYS

PRO

PHE

LYS

TYR

ASP

14

HIS

TYR

ASN

ILE

THR

TYR

LYS

PHE

ASN

15

GLY

PRO

THR

ASP

VAL

ALA

GLY

Entity 2, ZNH - C34 H32 N4 O4 Zn - 626.051 Da.

1

ZNH

Samples:

sample_1: sodium phosphate 50 mM; sodium chloride 100 mM; sodium azide 0.01%; IsdC, [U-100% 13C; U-100% 15N], 1.3 mM; ZNH 2.1 mM; D2O, [U-100% 2H], 7%; H2O 93%

sample_2: sodium phosphate 50 mM; sodium chloride 100 mM; sodium azide 0.01%; IsdC 1.1 mM; ZNH 2.3 mM; D2O 100%

sample_conditions_1: ionic strength: 150 mM; pH: 6; pressure: 1 atm; temperature: 302 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HNHA	sample_1	isotropic	sample_conditions_1
3D HCCH-COSY	sample_2	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNHB	sample_1	isotropic	sample_conditions_1

Software:

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement

PIPP, Garrett - peak picking

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

ATHNOS-CANDID, Herrmann, Guntert, Wuthrich - chemical shift assignment

CARA, Keller - chemical shift assignment

NMR spectrometers:

Bruker Avance 500 MHz
Bruker Avance 600 MHz
Bruker Avance 800 MHz

PDB	2K78 2O6P
DBJ	BAB42227 BAB57293 BAB94878 BAF67314 BAF78005
EMBL	CAG40106 CAG42839 CAI80683 CAQ49552 CBI49004
GB	AAL33767 AAW38020 ABD20415 ABD30198 ABQ48990
REF	WP_000789795 WP_000789808 WP_000789809 WP_000789810 WP_000789811
SP	A5IS17 A6QG32 A6U0U8 A7X149 A8Z1R1
AlphaFold	A5IS17 A6QG32 A6U0U8 A7X149 A8Z1R1