BMRB Entry 25342

Name: NMR structure of the protein YP_193882.1 from Lactobacillus acidophilus NCFM in presence of FMN
Published: 2014-12-08

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PDB ID: 2mwm
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR25342
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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 protein YP_193882.1 from Lactobacillus acidophilus NCFM in presence of FMN

Deposition date:

2014-11-13

Original release date:

2014-12-08

Authors:

Dutta, Samit; Serrano, Pedro; Geralt, Michael; Wuthrich, Kurt

Citation:

Citation: Dutta, Samit; Serrano, Pedro; Geralt, Michael; Wuthrich, Kurt. "NMR structure of the protein YP_193882.1 from Lactobacillus acidophilus NCFM in presence of FMN" .

Assembly members:

Assembly members:
entity, polymer, 151 residues, 17079.189 Da.
FLAVIN MONONUCLEOTIDE, non-polymer, 456.344 Da.

Natural source:

Natural source: Common Name: firmicutes Taxonomy ID: 272621 Superkingdom: Bacteria Kingdom: not available Genus/species: Lactobacillus acidophilus

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity: GMAKKTLILYYSWSGETKKM AEKINSEIKDSELKEVKVSE GTFDADMYKTSDIALDQIQG NKDFPEIQLDNIDYNNYDLI LIGSPVWSGYPATPIKTLLD QMKNYRGEVASFFTSAGTNH KAYVSHFNEWADGLNVIGVA RDDSEVDKWSK

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	1024
13C chemical shifts	607
15N chemical shifts	161

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity	1
2	Flavin Mononucleotide	2

Entities:

Entity 1, entity 151 residues - 17079.189 Da.

1

GLY

MET

ALA

LYS

THR

LEU

ILE

LEU

TYR

2

TYR

SER

TRP

SER

GLY

GLU

THR

LYS

MET

3

ALA

GLU

LYS

ILE

ASN

SER

GLU

ILE

LYS

ASP

4

SER

GLU

LEU

LYS

GLU

VAL

LYS

VAL

SER

GLU

5

GLY

THR

PHE

ASP

ALA

ASP

MET

TYR

LYS

THR

6

SER

ASP

ILE

ALA

LEU

ASP

GLN

ILE

GLN

GLY

7

ASN

LYS

ASP

PHE

PRO

GLU

ILE

GLN

LEU

ASP

8

ASN

ILE

ASP

TYR

ASN

TYR

ASP

LEU

ILE

9

LEU

ILE

GLY

SER

PRO

VAL

TRP

SER

GLY

TYR

10

PRO

ALA

THR

PRO

ILE

LYS

THR

LEU

ASP

11

GLN

MET

LYS

ASN

TYR

ARG

GLY

GLU

VAL

ALA

12

SER

PHE

THR

SER

ALA

GLY

THR

ASN

HIS

13

LYS

ALA

TYR

VAL

SER

HIS

PHE

ASN

GLU

TRP

14

ALA

ASP

GLY

LEU

ASN

VAL

ILE

GLY

VAL

ALA

15

ARG

ASP

SER

GLU

VAL

ASP

LYS

TRP

SER

16

LYS

Entity 2, Flavin Mononucleotide - C17 H21 N4 O9 P - 456.344 Da.

1

FMN

Samples:

sample_1: entity, [U-99% 13C; U-98% 15N], 1.2 mM; sodium phosphate 20 mM; sodium chloride 50 mM; sodium azide 5 mM; H2O 95%; D2O 5%

sample_conditions_1: temperature: 298 K; pH: 6.0; pressure: 1 atm; ionic strength: 0.0798 M

Experiments:

Name	Sample	Sample state	Sample conditions
APSY 4D-HACANH	sample_1	isotropic	sample_conditions_1
APSY 5D-HACACONH	sample_1	isotropic	sample_conditions_1
APSY 5D-CBCACONH	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1

Software:

CARA, Keller and Wuthrich - chemical shift assignment

CYANA v3.0, G ntert P., Herrmann, Guntert and Wuthrich - refinement, peak picking, chemical shift assignment, structure solution

TOPSPIN v3.1, Bruker Biospin - collection, processing

PROSA, Guntert - processing

OPAL, Luginbuhl, Guntert, Billeter and Wuthrich - geometry optimization

j-UNIO, Herrmann, Volk, Fiorito, Damberger, Guntert and Wuthrich - chemical shift assignment

NMR spectrometers:

Bruker Avance 600 MHz
Bruker Avance 800 MHz

PDB	3edo 2MWM 2N1M 3EDO
BMRB	25567
EMBL	CDF67787 CDF69462 CDF71219 CDF73047 CDF75037
GB	AAV42851 AGK94185 AJP46408 EEJ75695 KHE30356
REF	WP_003547179 WP_021874216 YP_193882