BMRB Entry 17749

Name: Solution NMR structure of Diiron protein in presence of 2 eq Zn2+, Northeast Structural Genomics Consortium Target OR21
Published: 2011-08-25

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PDB ID: 2lfd
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR17749
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution NMR structure of Diiron protein in presence of 2 eq Zn2+, Northeast Structural Genomics Consortium Target OR21

Deposition date:

2011-06-29

Original release date:

2011-08-25

Authors:

Wu, Yibing; Pires, Marcos; Mills, Jeffrey; Reig, Amanda; Szyperski, Thomas; DeGrado, William

Citation:

Citation: Wu, Yibing; Pires, Marcos; Mills, Jeffrey; Reig, Amanda; Szyperski, Thomas; DeGrado, William. "Solution NMR structure of Diiron protein in presence of 2 eq Zn2+" .

Assembly members:

Assembly members:
entity_1, polymer, 115 residues, 13489.420 Da.
ZIN, non-polymer, 236.269 Da.
ZN, non-polymer, 65.409 Da.

Natural source:

Natural source: Common Name: not available 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: BL21

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MDELRELLKAEQQGIKILKE VLKKAKEGDEQELARLNQEI VKAEKQGVKVYKEAAEKARN PEKRQVIDKILEDEEKHIEW HKAASKQGNAEQFASLVQQH LQDEQRHVEEIEKKN

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	407
15N chemical shifts	126
1H chemical shifts	869

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	7-(PYRIDIN-2-YLMETHYL)QUINOLIN-8-OL_1	2
3	7-(PYRIDIN-2-YLMETHYL)QUINOLIN-8-OL_2	2
4	Zinc ion 1	3
5	Zinc ion 2	3

Entities:

Entity 1, entity_1 115 residues - 13489.420 Da.

1

MET

ASP

GLU

LEU

ARG

GLU

LEU

LYS

ALA

2

GLU

GLN

GLY

ILE

LYS

ILE

LEU

LYS

GLU

3

VAL

LEU

LYS

ALA

LYS

GLU

GLY

ASP

GLU

4

GLN

GLU

LEU

ALA

ARG

LEU

ASN

GLN

GLU

ILE

5

VAL

LYS

ALA

GLU

LYS

GLN

GLY

VAL

LYS

VAL

6

TYR

LYS

GLU

ALA

GLU

LYS

ALA

ARG

ASN

7

PRO

GLU

LYS

ARG

GLN

VAL

ILE

ASP

LYS

ILE

8

LEU

GLU

ASP

GLU

LYS

HIS

ILE

GLU

TRP

9

HIS

LYS

ALA

SER

LYS

GLN

GLY

ASN

ALA

10

GLU

GLN

PHE

ALA

SER

LEU

VAL

GLN

HIS

11

LEU

GLN

ASP

GLU

GLN

ARG

HIS

VAL

GLU

12

ILE

GLU

LYS

ASN

Entity 2, 7-(PYRIDIN-2-YLMETHYL)QUINOLIN-8-OL_1 - C15 H12 N2 O - 236.269 Da.

1

ZIN

Entity 3, Zinc ion 1 - Zn - 65.409 Da.

1

ZN

Samples:

sample_1: entity_1, [U-100% 13C; U-100% 15N], 0.8 mM; H2O 95.0%; D2O 5.0%

sample_2: entity_1, [U-10% 13C; U-100% 15N], 0.3 mM; H2O 95.0%; D2O 5.0%

sample_conditions_1: ionic strength: 0.2 M; pH: 7.8; 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 CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D CCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D HN(CA)CO	sample_1	isotropic	sample_conditions_1
(4,3)D HCCH	sample_1	isotropic	sample_conditions_1
15N,13C-simNOESY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_1

Software:

AutoStruct, Huang, Tejero, Powers and Montelione - structure solution

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

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

XEASY, Bartels et al. - chemical shift assignment

PSVS, Bhattacharya and Montelione - structure solution

NMR spectrometers:

Varian INOVA 750 MHz
Varian INOVA 600 MHz