BMRB Entry 15139

Name: NMR structure of the E.coli protein NirD, Northeast Structural Genomics target ET100
Published: 2007-03-29

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PDB ID: 2jo6
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR15139
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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:

NMR structure of the E.coli protein NirD, Northeast Structural Genomics target ET100

Deposition date:

2007-02-21

Original release date:

2007-03-29

Authors:

Ramelot, Theresa; Cort, John; Yee, Adelinda; Guido, Valerie; Lukin, Jonathan; Arrowsmith, Cheryl; Kennedy, Michael

Citation:

Citation: Ramelot, Theresa; Cort, John; Yee, Adelinda; Arrowsmith, Cheryl; Kennedy, Michael. "NMR structure of E.coli NirD." .

Assembly members:

Assembly members:
NirD, polymer, 113 residues, 12750 Da.

Natural source:

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

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
NirD: QGHMSQWKDICKIDDILPET GVCALLGDEQVAIFRPYHSD QVFAISNIDPFFESSVLSRG LIAEHQGELWVASPLKKQRF RLSDGLCMEDEQFSVKHYEA RVKDGVVQLRGGS

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
spectral_peak_list

Data type	Count
13C chemical shifts	491
15N chemical shifts	119
1H chemical shifts	785

Time Domain Data

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	NirD	1

Entities:

Entity 1, NirD 113 residues - 12750 Da.

Three non-native residues at the N-terminus (QGH), were not included in the calculation. Two non-native residues at the C-terminus (GS), were included in the calculation.

1

GLN

GLY

HIS

MET

SER

GLN

TRP

LYS

ASP

ILE

2

CYS

LYS

ILE

ASP

ILE

LEU

PRO

GLU

THR

3

GLY

VAL

CYS

ALA

LEU

GLY

ASP

GLU

GLN

4

VAL

ALA

ILE

PHE

ARG

PRO

TYR

HIS

SER

ASP

5

GLN

VAL

PHE

ALA

ILE

SER

ASN

ILE

ASP

PRO

6

PHE

GLU

SER

VAL

LEU

SER

ARG

GLY

7

LEU

ILE

ALA

GLU

HIS

GLN

GLY

GLU

LEU

TRP

8

VAL

ALA

SER

PRO

LEU

LYS

GLN

ARG

PHE

9

ARG

LEU

SER

ASP

GLY

LEU

CYS

MET

GLU

ASP

10

GLU

GLN

PHE

SER

VAL

LYS

HIS

TYR

GLU

ALA

11

ARG

VAL

LYS

ASP

GLY

VAL

GLN

LEU

ARG

12

GLY

SER

Samples:

sample_1: protein, [U-100% 13C], 1 ± .2 mM; TRIS 10 ± 1 mM; sodium chloride 300 ± 5 mM; ZINC ION 10 ± 1 uM; DTT 10 ± 1 mM; sodium azide 0.01 ± 0.001 %; H2O 95%; D2O 5%

sample_2: protein, [U-100% 13C], 1 ± .2 mM; TRIS 10 ± 1 mM; sodium chloride 300 ± 5 mM; ZINC ION 10 ± 1 uM; DTT 10 ± 1 mM; sodium azide 0.01 ± 0.001 %; D2O 100%

sample_conditions_1: ionic strength: 300 mM; pH: 7.3; pressure: 1 atm; temperature: 293 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC (NH2 only)	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC (aliph)	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY (aliph)	sample_1	isotropic	sample_conditions_1
4D CC NOESY	sample_2	isotropic	sample_conditions_1
3D 1H-13C NOESY (arom)	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC (open)	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC (optimized)	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC (arom ct)	sample_1	isotropic	sample_conditions_1

Software:

AutoStruct v2.1.1, Huang, Swapana, Rajan, Ke, Xia, Shukla, Inouye and Montelione - data analysis

X-PLOR NIH v2.15.0, Schwieters, Kuszewski, Tjandra and Clore - structure solution

CNS v1.1, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

SPARKY v3.1, Goddard - peak picking

NMRPipe vlinux9, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMR spectrometers:

Varian INOVA 600 MHz
Varian INOVA 750 MHz