BMRB Entry 17282

Name: Solution Structure of apo-IscU(WT)
Published: 2012-08-29

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PDB ID: 2l4x
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR17282
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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 apo-IscU(WT)

Deposition date:

2010-11-03

Original release date:

2012-08-29

Authors:

Kim, Jin Hae; Tonelli, Marco; Markley, John

Citation:

Citation: Kim, Jin Hae; Tonelli, Marco; Kim, Taewook; Markley, John. "Three-dimensional structure and determinants of stability of the iron-sulfur cluster scaffold protein IscU from Escherichia coli." Biochemistry 51, 5557-5563 (2012).
PubMed: 22734684

Assembly members:

Assembly members:
IscU, polymer, 128 residues, 13865.679 Da.

Natural source:

Natural source: Common Name: E. coli Taxonomy ID: 562 Superkingdom: Bacteria Kingdom: not available Genus/species: Escherichia coli

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pTrc99a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
IscU: MAYSEKVIDHYENPRNVGSF DNNDENVGSGMVGAPACGDV MKLQIKVNDEGIIEDARFKT YGCGSAIASSSLVTEWVKGK SLDEAQAIKNTDIAEELELP PVKIHCSILAEDAIKAAIAD YKSKREAK

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
heteronucl_NOEs
- heteronuclear_noe_list_1
heteronucl_T1_relaxation
- heteronuclear_T1_list_1
heteronucl_T2_relaxation
- heteronuclear_T2_list_1
RDCs
- RDC_list_1

Data type	Count
13C chemical shifts	394
15N chemical shifts	98
1H chemical shifts	645
heteronuclear NOE values	81
residual dipolar couplings	74
T1 relaxation values	79
T2 relaxation values	79

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	IscU	1

Entities:

Entity 1, IscU 128 residues - 13865.679 Da.

1

MET

ALA

TYR

SER

GLU

LYS

VAL

ILE

ASP

HIS

2

TYR

GLU

ASN

PRO

ARG

ASN

VAL

GLY

SER

PHE

3

ASP

ASN

ASP

GLU

ASN

VAL

GLY

SER

GLY

4

MET

VAL

GLY

ALA

PRO

ALA

CYS

GLY

ASP

VAL

5

MET

LYS

LEU

GLN

ILE

LYS

VAL

ASN

ASP

GLU

6

GLY

ILE

GLU

ASP

ALA

ARG

PHE

LYS

THR

7

TYR

GLY

CYS

GLY

SER

ALA

ILE

ALA

SER

8

SER

LEU

VAL

THR

GLU

TRP

VAL

LYS

GLY

LYS

9

SER

LEU

ASP

GLU

ALA

GLN

ALA

ILE

LYS

ASN

10

THR

ASP

ILE

ALA

GLU

LEU

GLU

LEU

PRO

11

PRO

VAL

LYS

ILE

HIS

CYS

SER

ILE

LEU

ALA

12

GLU

ASP

ALA

ILE

LYS

ALA

ILE

ALA

ASP

13

TYR

LYS

SER

LYS

ARG

GLU

ALA

LYS

Samples:

15N-IscU: IscU, [U-15N], 0.7 – 0.8 mM; TRIS 20 mM; DTT 5 mM; sodium chloride 150 mM; DSS 0.7 mM; EDTA 0.5 mM; H2O 93%; D2O 7%

15N-13C-IscU: IscU, [U-13C; U-15N], 1.4 mM; TRIS 20 mM; DTT 5 mM; DSS 0.7 mM; sodium chloride 150 mM; EDTA 0.5 mM; H2O 93%; D2O 7%

15N-IscU_aniso: IscU, [U-15N], 0.7 – 0.8 mM; TRIS 20 mM; DTT 5 mM; sodium chloride 150 mM; DSS 0.7 mM; EDTA 0.5 mM; Pf1 phage 12 mg/ml; H2O 93%; D2O 7%

sample_conditions_1: ionic strength: 150 mM; pH: 8.0; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D 1H-15N NOESY	15N-13C-IscU	isotropic	sample_conditions_1
3D 1H-13C NOESY	15N-13C-IscU	isotropic	sample_conditions_1
2D 1H-15N HSQC	15N-IscU	isotropic	sample_conditions_1
2D 1H-13C HSQC	15N-13C-IscU	isotropic	sample_conditions_1
3D CBCA(CO)NH	15N-13C-IscU	isotropic	sample_conditions_1
3D C(CO)NH	15N-13C-IscU	isotropic	sample_conditions_1
3D HNCO	15N-13C-IscU	isotropic	sample_conditions_1
3D HNCACB	15N-13C-IscU	isotropic	sample_conditions_1
3D HBHA(CO)NH	15N-13C-IscU	isotropic	sample_conditions_1
3D H(CCO)NH	15N-13C-IscU	isotropic	sample_conditions_1
3D HCCH-TOCSY	15N-13C-IscU	isotropic	sample_conditions_1
2D IPAP 1H-15N HSQC	15N-IscU_aniso	anisotropic	sample_conditions_1

Software:

CYANA_3.0_intel v3.0_intel, P.GUNTERT ET AL. - refinement, structure solution

VNMRJ, Varian - collection

SPARKY, Goddard - chemical shift assignment, data analysis, peak picking

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

NMR spectrometers:

Varian INOVA 600 MHz
Varian INOVA 800 MHz
Varian INOVA 900 MHz
Bruker DMX 750 MHz

BMRB	15967 16245 16603 17836 17837 17844 18359 18360 18361 18362 18381 18750 18754
PDB	2KQK 2L4X 3LVL
DBJ	BAA16423 BAB36818 BAG78339 BAH64655 BAI26774
EMBL	CAD02745 CAP76981 CAQ32902 CAQ88187 CAQ99420
GB	AAC75582 AAG57643 AAL21436 AAN44075 AAN81505
PIR	AE0824
REF	NP_311422 NP_417024 NP_457073 NP_461477 NP_708368
SP	P0ACD4 P0ACD5 P0ACD6 P0ACD7
AlphaFold	P0ACD4 P0ACD5 P0ACD6 P0ACD7