BMRB Entry 15683

Name: Solution NMR Structure of the folded C-terminal fragment of YiaD from Escherichia coli, Northeast Structural Genomics Consortium Target ER553.
Published: 2008-03-19

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PDB ID: 2k1s
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR15683
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution NMR Structure of the folded C-terminal fragment of YiaD from Escherichia coli, Northeast Structural Genomics Consortium Target ER553.

Deposition date:

2008-03-14

Original release date:

2008-03-19

Authors:

Ramelot, Theresa; Zhao, Li; Hamilton, Kieth; Maglaqui, Melissa; Xiao, Rong; Liu, Jinfeng; Baran, Michael; Swapna, G.V.T.; Acton, Thomas; Rost, Burkhard; Montelione, Gaetano; Kennedy, Michael

Citation:

Citation: Ramelot, Theresa; Zhao, Li; Hamilton, Kieth; Maglaqui, Melissa; Xiao, Rong; Liu, Jinfeng; Baran, Michael; Swapna, G.V.T.; Acton, Thomas; Rost, Burkhard; Montelione, Gaetano; Kennedy, Michael. "Solution NMR Structure of the folded C-terminal fragment of YiaD from Escherichia coli. Northeast Structural Genomics Consortium Target ER553." .

Assembly members:

Assembly members:
YiaD, polymer, 149 residues, 16056.109 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: pET21

Entity Sequences (FASTA):

Entity Sequences (FASTA):
YiaD: YYMDVQEAKLRDKMRGTGVS VTRSGDNIILNMPNNVTFDS SSATLKPAGANTLTGVAMVL KEYPKTAVNVIGYTDSTGGH DLNMRLSQQRADSVASALIT QGVDASRIRTQGLGPANPIA SNSTAEGKAQNRRVEITLSP LLEHHHHHH

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
spectral_peak_list

Data type	Count
13C chemical shifts	596
15N chemical shifts	161
1H chemical shifts	998

Time Domain Data

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	YiaD	1

Entities:

Entity 1, YiaD 149 residues - 16056.109 Da.

C-terminal residues 59-199 of YiaD followed by 8 non-native C-terminal residues (LEHHHH)

1

TYR

MET

ASP

VAL

GLN

GLU

ALA

LYS

LEU

2

ARG

ASP

LYS

MET

ARG

GLY

THR

GLY

VAL

SER

3

VAL

THR

ARG

SER

GLY

ASP

ASN

ILE

LEU

4

ASN

MET

PRO

ASN

VAL

THR

PHE

ASP

SER

5

SER

ALA

THR

LEU

LYS

PRO

ALA

GLY

ALA

6

ASN

THR

LEU

THR

GLY

VAL

ALA

MET

VAL

LEU

7

LYS

GLU

TYR

PRO

LYS

THR

ALA

VAL

ASN

VAL

8

ILE

GLY

TYR

THR

ASP

SER

THR

GLY

HIS

9

ASP

LEU

ASN

MET

ARG

LEU

SER

GLN

ARG

10

ALA

ASP

SER

VAL

ALA

SER

ALA

LEU

ILE

THR

11

GLN

GLY

VAL

ASP

ALA

SER

ARG

ILE

ARG

THR

12

GLN

GLY

LEU

GLY

PRO

ALA

ASN

PRO

ILE

ALA

13

SER

ASN

SER

THR

ALA

GLU

GLY

LYS

ALA

GLN

14

ASN

ARG

VAL

GLU

ILE

THR

LEU

SER

PRO

15

LEU

GLU

HIS

Samples:

NC_sample: entity, [U-100% 13C; U-100% 15N], 1.9 ± .1 mM; MES 20 ± 1 mM; sodium chloride 100 ± 5 mM; calcium chloride 5 ± 0.2 mM; DTT 10 ± .5 mM; sodium azide 0.02 ± 0.001 %

NC5_sample: entity, [U-5% 13C; U-100% 15N], 1.3 ± .1 mM; MES 20 ± 1 mM; sodium chloride 100 ± 5 mM; calcium chloride 5 ± 0.2 mM; DTT 10 ± .5 mM; sodium azide 0.02 ± 0.001 %

NC_sample_in_D2O: entity, [U-100% 13C; U-100% 15N], 1.9 ± .1 mM; MES 20 ± 1 mM; sodium chloride 100 ± 5 mM; calcium chloride 5 ± 0.2 mM; DTT 10 ± .5 mM; sodium azide 0.02 ± 0.001 %

sample_conditions_1: ionic strength: 0.1 M; pH: 6.5; pressure: 1 atm; temperature: 293 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	NC_sample	isotropic	sample_conditions_1
2D 1H-13C HSQC (arom ct)	NC_sample	isotropic	sample_conditions_1
2D 1H-13C HSQC	NC5_sample	isotropic	sample_conditions_1
3D 1H-15N NOESY	NC_sample	isotropic	sample_conditions_1
3D 1H-13C NOESY	NC_sample	isotropic	sample_conditions_1
3D 1H-13C NOESY	NC_sample_in_D2O	isotropic	sample_conditions_1
3D HNCO	NC_sample	isotropic	sample_conditions_1
3D HNCA	NC_sample	isotropic	sample_conditions_1
3D HN(CO)CA	NC_sample	isotropic	sample_conditions_1
3D HNCACB	NC_sample	isotropic	sample_conditions_1
3D CBCA(CO)NH	NC_sample	isotropic	sample_conditions_1
3D C(CO)NH	NC_sample	isotropic	sample_conditions_1
3D HBHA(CO)NH	NC_sample	isotropic	sample_conditions_1
3D H(CCO)NH	NC_sample	isotropic	sample_conditions_1
3D HCCH-TOCSY	NC_sample	isotropic	sample_conditions_1
3D HCCH-COSY	NC_sample	isotropic	sample_conditions_1
4D CC NOESY	NC_sample_in_D2O	isotropic	sample_conditions_1
2D 1H-13C HSQC (arom no ct)	NC_sample	isotropic	sample_conditions_1

Software:

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

VNMR v6.1C, Varian - collection

TOPSPIN v2.1, Bruker Biospin - collection

AutoStruct v2.1.1, Huang, Tejero, Powers 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 v3.113, Goddard - data analysis

PSVS v1.3, Bhattacharya and Montelione - structure solution

AutoAssign, Zimmerman, Moseley, Kulikowski and Montelione - chemical shift assignment

NMR spectrometers:

Varian INOVA 600 MHz
Bruker AvanceIII 850 MHz

PDB	2K1S 2N48
DBJ	BAB37860 BAE77743 BAG79349 BAI28203 BAI33377
EMBL	CAP78012 CAQ33870 CAR00514 CAR05180 CAR10226
GB	AAB18529 AAG58701 AAN45037 AAN82806 AAP19151
REF	NP_312464 NP_709330 WP_000470321 WP_000495106 WP_000747546
SP	P37665
AlphaFold	P37665