BMRB Entry 19417

Name: NMR solution structure of oxidised PaDsbA
Published: 2014-11-10

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PDB ID: 2mbt
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR19417
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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:

NMR solution structure of oxidised PaDsbA

Deposition date:

2013-08-08

Original release date:

2014-11-10

Authors:

Rimmer, Kieran; Mohanty, Biswaranjan; Scanlon, Martin

Citation:

Citation: Rimmer, Kieran; Mohanty, Biswaranjan; Headey, Stephen; Vazirani, Mansha; Shouldice, Stephen; Morton, Craig; Martin, Jennifer; Simpson, Jamie; Scanlon, Martin. "The DsbA oxidoreductase from Pseudomonas aeruginosa binds ligands at a site alternate to other DsbAs" PLOS One ., .-..

Assembly members:

Assembly members:
entity, polymer, 190 residues, 21152.434 Da.

Natural source:

Natural source: Common Name: Pseudomonas aeruginosa Taxonomy ID: 287 Superkingdom: Bacteria Kingdom: not available Genus/species: Pseudomonas aeruginosa

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET28a-PaDsbA

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity: GDDYTAGKEYVELSSPVPVS QPGKIEVVELFWYGCPHCYA FEPTIVPWSEKLPADVHFVR LPALFGGIWNVHGQMFLTLE SMGVEHDVHNAVFEAIHKEH KKLATPEEMADFLAGKGVDK EKFLSTYNSFAIKGQMEKAK KLAMAYQVTGVPTMVVNGKY RFDIGSAGGPEETLKLADYL IEKERAAAKK

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	591
15N chemical shifts	176
1H chemical shifts	1221

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	PaDsbA	1

Entities:

Entity 1, PaDsbA 190 residues - 21152.434 Da.

1	GLY	ASP	ASP	TYR	THR	ALA	GLY	LYS	GLU	TYR
2	VAL	GLU	LEU	SER	SER	PRO	VAL	PRO	VAL	SER
3	GLN	PRO	GLY	LYS	ILE	GLU	VAL	VAL	GLU	LEU
4	PHE	TRP	TYR	GLY	CYS	PRO	HIS	CYS	TYR	ALA
5	PHE	GLU	PRO	THR	ILE	VAL	PRO	TRP	SER	GLU
6	LYS	LEU	PRO	ALA	ASP	VAL	HIS	PHE	VAL	ARG
7	LEU	PRO	ALA	LEU	PHE	GLY	GLY	ILE	TRP	ASN
8	VAL	HIS	GLY	GLN	MET	PHE	LEU	THR	LEU	GLU
9	SER	MET	GLY	VAL	GLU	HIS	ASP	VAL	HIS	ASN
10	ALA	VAL	PHE	GLU	ALA	ILE	HIS	LYS	GLU	HIS
11	LYS	LYS	LEU	ALA	THR	PRO	GLU	GLU	MET	ALA
12	ASP	PHE	LEU	ALA	GLY	LYS	GLY	VAL	ASP	LYS
13	GLU	LYS	PHE	LEU	SER	THR	TYR	ASN	SER	PHE
14	ALA	ILE	LYS	GLY	GLN	MET	GLU	LYS	ALA	LYS
15	LYS	LEU	ALA	MET	ALA	TYR	GLN	VAL	THR	GLY
16	VAL	PRO	THR	MET	VAL	VAL	ASN	GLY	LYS	TYR
17	ARG	PHE	ASP	ILE	GLY	SER	ALA	GLY	GLY	PRO
18	GLU	GLU	THR	LEU	LYS	LEU	ALA	ASP	TYR	LEU
19	ILE	GLU	LYS	GLU	ARG	ALA	ALA	ALA	LYS	LYS

Samples:

sample_1: PaDsbA, [U-100% 13C; U-100% 15N], 2 mM; sodium phosphate 50 mM; sodium chloride 50 mM; sodium azide 0.02%; D2O, [U-100% 2H], 10%; DSS 1 mM

sample_conditions_1: pH: 7.4; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	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:

CYANA v3.0, Guntert, Mumenthaler and Wuthrich - structure solution

OPALp, Luginbuhl, Guntert, Billeter and Wuthrich - refinement

UNIO, Herrmann, Guntert and Wuthrich - chemical shift assignment

NMR spectrometers:

Bruker Avance 800 MHz
Bruker Avance 600 MHz
Bruker Avance 500 MHz

BMRB	19414
PDB	2MBT 2MBU
DBJ	BAK93072 BAP25402 BAP54200 BAQ43440 BAR70987
EMBL	CAW30639 CCQ84537 CDH74254 CDH80603 CDI94111
GB	AAB41795 AAD22452 AAG08874 AAT49872 ABJ14875
REF	NP_254176 WP_003096976 WP_003155460 WP_009316028 WP_012078052
SP	P0C2B2 Q02DM0
AlphaFold	P0C2B2 Q02DM0

1	GLY	ASP	ASP	TYR	THR	ALA	GLY	LYS	GLU	TYR
2	VAL	GLU	LEU	SER	SER	PRO	VAL	PRO	VAL	SER
3	GLN	PRO	GLY	LYS	ILE	GLU	VAL	VAL	GLU	LEU
4	PHE	TRP	TYR	GLY	CYS	PRO	HIS	CYS	TYR	ALA
5	PHE	GLU	PRO	THR	ILE	VAL	PRO	TRP	SER	GLU
6	LYS	LEU	PRO	ALA	ASP	VAL	HIS	PHE	VAL	ARG
7	LEU	PRO	ALA	LEU	PHE	GLY	GLY	ILE	TRP	ASN
8	VAL	HIS	GLY	GLN	MET	PHE	LEU	THR	LEU	GLU
9	SER	MET	GLY	VAL	GLU	HIS	ASP	VAL	HIS	ASN
10	ALA	VAL	PHE	GLU	ALA	ILE	HIS	LYS	GLU	HIS
11	LYS	LYS	LEU	ALA	THR	PRO	GLU	GLU	MET	ALA
12	ASP	PHE	LEU	ALA	GLY	LYS	GLY	VAL	ASP	LYS
13	GLU	LYS	PHE	LEU	SER	THR	TYR	ASN	SER	PHE
14	ALA	ILE	LYS	GLY	GLN	MET	GLU	LYS	ALA	LYS
15	LYS	LEU	ALA	MET	ALA	TYR	GLN	VAL	THR	GLY
16	VAL	PRO	THR	MET	VAL	VAL	ASN	GLY	LYS	TYR
17	ARG	PHE	ASP	ILE	GLY	SER	ALA	GLY	GLY	PRO
18	GLU	GLU	THR	LEU	LYS	LEU	ALA	ASP	TYR	LEU
19	ILE	GLU	LYS	GLU	ARG	ALA	ALA	ALA	LYS	LYS

1	GLY	ASP	ASP	TYR	THR	ALA	GLY	LYS	GLU	TYR
2	VAL	GLU	LEU	SER	SER	PRO	VAL	PRO	VAL	SER
3	GLN	PRO	GLY	LYS	ILE	GLU	VAL	VAL	GLU	LEU
4	PHE	TRP	TYR	GLY	CYS	PRO	HIS	CYS	TYR	ALA
5	PHE	GLU	PRO	THR	ILE	VAL	PRO	TRP	SER	GLU
6	LYS	LEU	PRO	ALA	ASP	VAL	HIS	PHE	VAL	ARG
7	LEU	PRO	ALA	LEU	PHE	GLY	GLY	ILE	TRP	ASN
8	VAL	HIS	GLY	GLN	MET	PHE	LEU	THR	LEU	GLU
9	SER	MET	GLY	VAL	GLU	HIS	ASP	VAL	HIS	ASN
10	ALA	VAL	PHE	GLU	ALA	ILE	HIS	LYS	GLU	HIS
11	LYS	LYS	LEU	ALA	THR	PRO	GLU	GLU	MET	ALA
12	ASP	PHE	LEU	ALA	GLY	LYS	GLY	VAL	ASP	LYS
13	GLU	LYS	PHE	LEU	SER	THR	TYR	ASN	SER	PHE
14	ALA	ILE	LYS	GLY	GLN	MET	GLU	LYS	ALA	LYS
15	LYS	LEU	ALA	MET	ALA	TYR	GLN	VAL	THR	GLY
16	VAL	PRO	THR	MET	VAL	VAL	ASN	GLY	LYS	TYR
17	ARG	PHE	ASP	ILE	GLY	SER	ALA	GLY	GLY	PRO
18	GLU	GLU	THR	LEU	LYS	LEU	ALA	ASP	TYR	LEU
19	ILE	GLU	LYS	GLU	ARG	ALA	ALA	ALA	LYS	LYS