BMRB Entry 16098

Name: Solution structure of Apo-form YjaB from Escherichia coli
Published: 2009-04-17

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PDB ID: 2kcw
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/BMR16098
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution structure of Apo-form YjaB from Escherichia coli

Deposition date:

2008-12-30

Original release date:

2009-04-17

Authors:

Lu, Jie; Wang, Xu; Jin, Changwen

Citation:

Citation: Lu, Jie; Wang, Xu; Xia, Bin; Jin, Changwen. "Solution structure of Apo-YjaB form Escherichia coli" Proteins 76, 261-265 (2009).
PubMed: 19343803

Assembly members:

Assembly members:
Apo-form YjaB, polymer, 147 residues, 16464.789 Da.

Natural source:

Natural source: Common Name: E. coli 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: pET28a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Apo-form YjaB: MVISIRRSRHEEGEELVAIW CRSVDATHDFLSAEYRTELE DLVRSFLPEAPLWVAVNERD QPVGFMLLSGQHMDALFIDP DVRGCGVGRVLVEHALSMAP ELTTNVNEQNEQAVGFYKKV GFKVTGRSEVDDLGKPYPLL NLAYVGA

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	622
15N chemical shifts	146
1H chemical shifts	1013

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Apo-form YjaB	1

Entities:

Entity 1, Apo-form YjaB 147 residues - 16464.789 Da.

1

MET

VAL

ILE

SER

ILE

ARG

SER

ARG

HIS

2

GLU

GLY

GLU

LEU

VAL

ALA

ILE

TRP

3

CYS

ARG

SER

VAL

ASP

ALA

THR

HIS

ASP

PHE

4

LEU

SER

ALA

GLU

TYR

ARG

THR

GLU

LEU

GLU

5

ASP

LEU

VAL

ARG

SER

PHE

LEU

PRO

GLU

ALA

6

PRO

LEU

TRP

VAL

ALA

VAL

ASN

GLU

ARG

ASP

7

GLN

PRO

VAL

GLY

PHE

MET

LEU

SER

GLY

8

GLN

HIS

MET

ASP

ALA

LEU

PHE

ILE

ASP

PRO

9

ASP

VAL

ARG

GLY

CYS

GLY

VAL

GLY

ARG

VAL

10

LEU

VAL

GLU

HIS

ALA

LEU

SER

MET

ALA

PRO

11

GLU

LEU

THR

ASN

VAL

ASN

GLU

GLN

ASN

12

GLU

GLN

ALA

VAL

GLY

PHE

TYR

LYS

VAL

13

GLY

PHE

LYS

VAL

THR

GLY

ARG

SER

GLU

VAL

14

ASP

LEU

GLY

LYS

PRO

TYR

PRO

LEU

15

ASN

LEU

ALA

TYR

VAL

GLY

ALA

Samples:

sample_1: TRIS 30 mM; sodium chloride 100 mM; DTT 10 mM; YjaB protein, [U-13C; U-15N], 1 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 130 mM; pH: 7.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1

Software:

NMRPipe v2.1, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRView v5, Johnson, One Moon Scientific - data analysis

xwinnmr v3.5, Bruker Biospin - collection

CYANA v2.0, Guntert, Mumenthaler and Wuthrich - structure solution

AMBER v7, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - structure refinement

NMR spectrometers:

Bruker Avance 600 MHz

PDB	2KCW
DBJ	BAE78014 BAI28268 BAI33451 BAI38569 BAJ45724
EMBL	CAA26570 CAQ34361 CAR00982 CAV01265 CBJ03773
GB	AAC43106 AAC76982 AAZ90685 ABB64225 ABV08412
REF	NP_418436 WP_000236960 WP_000236962 WP_000236972 WP_000236973
SP	P09163
AlphaFold	P09163