BMRB Entry 15167

Name: NMR Structure of E. Coli YehR Protein. Northeast Structural Genomics Target ER538.
Published: 2007-04-11

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PDB ID: 2joe
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR15167
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:

NMR Structure of E. Coli YehR Protein. Northeast Structural Genomics Target ER538.

Deposition date:

2007-03-08

Original release date:

2007-04-11

Authors:

Ding, Keyang; Ramelot, Theresa; Cort, John; Chen, Chen; Jiang, Mei; Cunningham, Kellie; Ma, Li-Chung; Xiao, Rong; Liu, Jinfeng; Baran, Michael; Swapna, Gurla; Acton, Thomas; Rost, Burkhard; Montelione, Gaetano; Kennedy, Michael

Citation:

Citation: Ding, Keyang; Ramelot, Theresa; Cort, John; Jiang, Mei; Xiao, Rong; Swapna, Gurla; Montelione, Gaetano; Kennedy, Michael. "NMR Structure of E. Coli YehR Protein" .

Assembly members:

Assembly members:
YehR, polymer, 139 residues, 15389.607 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: pET21

Entity Sequences (FASTA):

Entity Sequences (FASTA):
YehR: MGDKEESKKFSANLNGTEIA ITYVYKGDKVLKQSSETKIQ FASIGATTKEDAAKTLEPLS AKYKNIAGVEEKLTYTDTYA QENVTIDMEKVDFKALQGIS GINVSAEDAKKGITMAQMEL VMKAAGFKEVKLEHHHHHH

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
spectral_peak_list

Data type	Count
13C chemical shifts	611
15N chemical shifts	147
1H chemical shifts	974

Time Domain Data

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	YehR	1

Entities:

Entity 1, YehR 139 residues - 15389.607 Da.

The C-terminal his-tag LEHHHHHH was included in calculation. The N-terminal 22 residues MKAFNKLFSLVVASVLVFSLAG was not included in the cloning.

1

MET

GLY

ASP

LYS

GLU

SER

LYS

PHE

2

SER

ALA

ASN

LEU

ASN

GLY

THR

GLU

ILE

ALA

3

ILE

THR

TYR

VAL

TYR

LYS

GLY

ASP

LYS

VAL

4

LEU

LYS

GLN

SER

GLU

THR

LYS

ILE

GLN

5

PHE

ALA

SER

ILE

GLY

ALA

THR

LYS

GLU

6

ASP

ALA

LYS

THR

LEU

GLU

PRO

LEU

SER

7

ALA

LYS

TYR

LYS

ASN

ILE

ALA

GLY

VAL

GLU

8

GLU

LYS

LEU

THR

TYR

THR

ASP

THR

TYR

ALA

9

GLN

GLU

ASN

VAL

THR

ILE

ASP

MET

GLU

LYS

10

VAL

ASP

PHE

LYS

ALA

LEU

GLN

GLY

ILE

SER

11

GLY

ILE

ASN

VAL

SER

ALA

GLU

ASP

ALA

LYS

12

LYS

GLY

ILE

THR

MET

ALA

GLN

MET

GLU

LEU

13

VAL

MET

LYS

ALA

GLY

PHE

LYS

GLU

VAL

14

LYS

LEU

GLU

HIS

Samples:

sample_1: protein, [U-100% 13C; U-100% 15N], 1 ± 0.2 mM; NH4OAc 20 ± 1 mM; NaCl 100 ± 5 mM; DTT 10 ± 1 mM; CaCl2 5 ± 1 mM; NaN3 0.02 ± 0.001 %; H2O 95 ± 0.001 %; D2O 5 ± 0.001 %

sample_2: protein, [U-5% 13C; U-100% 15N], 1 ± 0.2 mM; NH4OAc 20 ± 1 mM; NaCl 100 ± 5 mM; DTT 10 ± 1 mM; CaCl2 5 ± 1 mM; NaN3 0.02 ± 0.001 %; H2O 95 ± 0.001 %; D2O 5 ± 0.001 %

sample_3: protein, [U-100% 13C; U-100% 15N], 1 ± 0.2 mM; NH4OAc 20 ± 1 mM; NaCl 100 ± 5 mM; DTT 10 ± 1 mM; CaCl2 5 ± 1 mM; NaN3 0.02 ± 0.001 %; D2O 100 ± 0.001 %

sample_conditions_1: ionic strength: 100 mM; pH: 5.5; pressure: 1 atm; temperature: 283 K

sample_conditions_2: ionic strength: 100 mM; pH: 5.5; pressure: 1 atm; temperature: 293 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_2
3D HNCO	sample_1	isotropic	sample_conditions_2
3D HNCA	sample_1	isotropic	sample_conditions_2
3D HN(CO)CA	sample_1	isotropic	sample_conditions_2
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_2
3D HNCACB	sample_1	isotropic	sample_conditions_2
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_2
3D HNHA	sample_2	isotropic	sample_conditions_2
3D C(CO)NH	sample_1	isotropic	sample_conditions_2
3D H(CCO)NH	sample_1	isotropic	sample_conditions_2
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_2
2D 1H-13C HSQC	sample_3	isotropic	sample_conditions_2
2D 1H-13C (Arom) HSQC	sample_1	isotropic	sample_conditions_2
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-15N (NH2) HSQC	sample_1	isotropic	sample_conditions_2
3D 1H-15N NOESY	sample_2	isotropic	sample_conditions_1
3D 1H-13C (Aliph) NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C (Arom) NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C (Aliph) NOESY	sample_3	isotropic	sample_conditions_2
4D 1H-13C NOESY	sample_3	isotropic	sample_conditions_2
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_1

Software:

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

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

NMR spectrometers:

Varian INOVA 750 MHz
Varian INOVA 600 MHz
Varian INOVA 500 MHz

PDB	2JOE
DBJ	BAB19552 BAB36357 BAE76599 BAG66588 BAG77915
EMBL	CAP76626 CAQ32527 CAQ99044 CAR03550 CAR08661
GB	AAA60486 AAC75184 AAG57191 AAN43719 AAN81109
PRF	2014253T
REF	NP_310961 NP_416627 NP_708012 WP_000293099 WP_000397950
SP	P33354
AlphaFold	P33354