BMRB Entry 6868

Name: Solution Structure of ydhR protein from Escherichia coli
Published: 2006-04-17

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PDB ID: 2asy
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR6868
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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 ydhR protein from Escherichia coli

Deposition date:

2005-10-20

Original release date:

2006-04-17

Authors:

Revington, M.; Shaw, G.

Citation:

Citation: Revington, M.; Semesi, A.; Yee, A.; Shaw, G.. "Solution structure of the Escherichia coli protein ydhR: a putative mono-oxygenase" Protein Sci. 14, 3115-3120 (2005).
PubMed: 16260765

Assembly members:

Assembly members:
Protein ydhR precursor, polymer, 123 residues, Formula weight is not available

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Protein ydhR precursor: MGTSHHHHHHSSGRENLYFQ GHMATLLQLHFAFNGPFGDA MAEQLKPLAESINQEPGFLW KVWTESEKNHEAGGIYLFTD EKSALAYLEKHTARLKNLGV EEVVAKVFDVNEPLSQINQA KLA

Data sets:

assigned_chemical_shifts
- chemical_shift_set_1

Data type	Count
13C chemical shifts	427
15N chemical shifts	108
1H chemical shifts	690

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Protein ydhR precursor, chain A	1
2	Protein ydhR precursor, chain B	1

Entities:

Entity 1, Protein ydhR precursor, chain A 123 residues - Formula weight is not available

1

MET

GLY

THR

SER

HIS

2

SER

GLY

ARG

GLU

ASN

LEU

TYR

PHE

GLN

3

GLY

HIS

MET

ALA

THR

LEU

GLN

LEU

HIS

4

PHE

ALA

PHE

ASN

GLY

PRO

PHE

GLY

ASP

ALA

5

MET

ALA

GLU

GLN

LEU

LYS

PRO

LEU

ALA

GLU

6

SER

ILE

ASN

GLN

GLU

PRO

GLY

PHE

LEU

TRP

7

LYS

VAL

TRP

THR

GLU

SER

GLU

LYS

ASN

HIS

8

GLU

ALA

GLY

ILE

TYR

LEU

PHE

THR

ASP

9

GLU

LYS

SER

ALA

LEU

ALA

TYR

LEU

GLU

LYS

10

HIS

THR

ALA

ARG

LEU

LYS

ASN

LEU

GLY

VAL

11

GLU

VAL

ALA

LYS

VAL

PHE

ASP

VAL

12

ASN

GLU

PRO

LEU

SER

GLN

ILE

ASN

GLN

ALA

13

LYS

LEU

ALA

Samples:

sample_1: Protein ydhR precursor, [U-15N; U-13C], 0.5 mM; MES 25 mM; NaCl 450 mM; Sodium Azide 0.01%; H2O 90%; D2O 10%

sample_2: Protein ydhR precursor, [U-15N; U-13C], 0.5 mM; MES 25 mM; NaCl 450 mM; Sodium Azide 0.01%; D2O 100%

sample_cond_1: ionic strength: 450 mM; pH: 6.5; pressure: 1 atm; temperature: 303 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D 15N-separated NOESY	not available	not available	not available
3D 13C-aliphatic region-separated NOESY	not available	not available	not available
3D 13C-aromatic region-separated NOESY	not available	not available	not available

Software:

VNMR v6.1B - collection

NMRPipe v2.3 - processing

NMRView v5.2.2 - data analysis

CYANA v2.032.3 - refinement

CNS v1.1 - structure solution

NMR spectrometers:

Varian INOVA 600 MHz

PDB	1WD6 2ASY 2HIQ
DBJ	BAB35797 BAE76495 BAG77313 BAI25642 BAI30616
EMBL	CAP76164 CAQ32143 CAQ98575 CAR03026 CAR13152
GB	AAB47943 AAC74737 AAG56654 AAN43273 AAP17161
REF	NP_288101 NP_310401 NP_416182 NP_707566 NP_837352
SP	P0ACX3 P0ACX4
AlphaFold	P0ACX3 P0ACX4