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BMRB: 19417

2MBT

NMR solution structure of oxidised PaDsbA

Authors

Rimmer, K., Mohanty, B., Scanlon, M.J.

Assembly

PaDsbA

Entity

1. PaDsbA (polymer, Thiol state: all disulfide bound), 190 monomers, 21124.00 Da Detail

GDDYTAGKEY VELSSPVPVS QPGKIEVVEL FWYGCPHCYA FEPTIVPWSE KLPADVHFVR LPALFGGIWN VHGQMFLTLE SMGVEHDVHN AVFEAIHKEH KKLATPEEMA DFLAGKGVDK EKFLSTYNSF AIKGQMEKAK KLAMAYQVTG VPTMVVNGKY RFDIGSAGGP EETLKLADYL IEKERAAAKK

Formula weight

21124.0 Da

Entity Connection

disulfide 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS35:SG	1:CYS38:SG

Source organism

Pseudomonas aeruginosa

Exptl. method

Refine. method

water refinement

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.4 %, Completeness: 81.4 %, Completeness (bb): 82.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	81.4 % (1815 of 2230)	87.4 % (1009 of 1154)	71.2 % (631 of 886)	92.1 % (175 of 190)
Backbone	82.0 % (917 of 1118)	93.2 % (359 of 385)	70.9 % (393 of 554)	92.2 % (165 of 179)
Sidechain	83.0 % (1068 of 1286)	84.5 % (650 of 769)	80.6 % (408 of 506)	90.9 % (10 of 11)
Aromatic	64.9 % (148 of 228)	77.2 % (88 of 114)	51.4 % (57 of 111)	100.0 % (3 of 3)
Methyl	96.6 % (197 of 204)	96.1 % (98 of 102)	97.1 % (99 of 102)

1. entity

GDDYTAGKEY VELSSPVPVS QPGKIEVVEL FWYGCPHCYA FEPTIVPWSE KLPADVHFVR LPALFGGIWN VHGQMFLTLE SMGVEHDVHN AVFEAIHKEH KKLATPEEMA DFLAGKGVDK EKFLSTYNSF AIKGQMEKAK KLAMAYQVTG VPTMVVNGKY RFDIGSAGGP EETLKLADYL IEKERAAAKK

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	PaDsbA	[U-100% 13C; U-100% 15N]		2 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		0.02 %
5	D2O	[U-100% 2H]		10 %
6	DSS	natural abundance		1 mM

LACS Plot; CA

Referencing offset: 0.06 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: 0.06 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.04 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2MBT, Strand ID: A Detail

Release date

2014-11-09

Citation

The DsbA oxidoreductase from Pseudomonas aeruginosa binds ligands at a site alternate to other DsbAs
Rimmer, K., Mohanty, B., Headey, S.J., Vazirani, M., Shouldice, S.R., Morton, C., Martin, J.L., Simpson, J.S., Scanlon, M.J.
PLOS One

Related entities 1. PaDsbA, : 1 : 1 : 6 : 117 entities Detail

Experiments performed 9 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	PaDsbA	[U-100% 13C; U-100% 15N]		2 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		0.02 %
5	D2O	[U-100% 2H]		10 %
6	DSS	natural abundance		1 mM

2 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	PaDsbA	[U-100% 13C; U-100% 15N]		2 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		0.02 %
5	D2O	[U-100% 2H]		10 %
6	DSS	natural abundance		1 mM

3 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	PaDsbA	[U-100% 13C; U-100% 15N]		2 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		0.02 %
5	D2O	[U-100% 2H]		10 %
6	DSS	natural abundance		1 mM

4 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	PaDsbA	[U-100% 13C; U-100% 15N]		2 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		0.02 %
5	D2O	[U-100% 2H]		10 %
6	DSS	natural abundance		1 mM

5 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	PaDsbA	[U-100% 13C; U-100% 15N]		2 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		0.02 %
5	D2O	[U-100% 2H]		10 %
6	DSS	natural abundance		1 mM

6 3D HBHA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	PaDsbA	[U-100% 13C; U-100% 15N]		2 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		0.02 %
5	D2O	[U-100% 2H]		10 %
6	DSS	natural abundance		1 mM

7 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	PaDsbA	[U-100% 13C; U-100% 15N]		2 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		0.02 %
5	D2O	[U-100% 2H]		10 %
6	DSS	natural abundance		1 mM

8 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	PaDsbA	[U-100% 13C; U-100% 15N]		2 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		0.02 %
5	D2O	[U-100% 2H]		10 %
6	DSS	natural abundance		1 mM

9 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	PaDsbA	[U-100% 13C; U-100% 15N]		2 mM
2	sodium phosphate	natural abundance		50 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		0.02 %
5	D2O	[U-100% 2H]		10 %
6	DSS	natural abundance		1 mM

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_19417_2mbt.nef
Input source #2: Coordindates	2mbt.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:37:CYS:SG	A:40:CYS:SG	oxidized, CA 51.825, CB 45.562 ppm	oxidized, CA 63.756, CB 34.132 ppm	2.044

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

------10--------20--------30--------40--------50--------60--------70--------80--------90-------100--
GDDYTAGKEYVELSSPVPVSQPGKIEVVELFWYGCPHCYAFEPTIVPWSEKLPADVHFVRLPALFGGIWNVHGQMFLTLESMGVEHDVHNAVFEAIHKEH
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GDDYTAGKEYVELSSPVPVSQPGKIEVVELFWYGCPHCYAFEPTIVPWSEKLPADVHFVRLPALFGGIWNVHGQMFLTLESMGVEHDVHNAVFEAIHKEH
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-----110-------120-------130-------140-------150-------160-------170-------180-------190--
KKLATPEEMADFLAGKGVDKEKFLSTYNSFAIKGQMEKAKKLAMAYQVTGVPTMVVNGKYRFDIGSAGGPEETLKLADYLIEKERAAAKK
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
KKLATPEEMADFLAGKGVDKEKFLSTYNSFAIKGQMEKAKKLAMAYQVTGVPTMVVNGKYRFDIGSAGGPEETLKLADYLIEKERAAAKK
-------110-------120-------130-------140-------150-------160-------170-------180-------190

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	190	0	0	100.0

Content subtype: combined_19417_2mbt.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	1		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1776		97.4 (chain: A, length: 190)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	3533 (1)	noe	96.3 (chain: A, length: 190)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 190, Sequence coverage: 97.4%
- Total number of assignments
  - ¹H chemical shifts: 1009
  - ¹³C chemical shifts: 591
  - ¹⁵N chemical shifts: 176
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 190, Sequence coverage: 96.3%
- Total number of restraints: 3533
- Weight of restraints: 1.0 (3533)
- Potential type of restraints: upper-bound-parabolic (3533)
- Range of distance target values: 2.41, 5.5 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Keywords DsbA, oxidised, oxidoreductase, Pseudomonas aeruginosa