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BMRB: 34576

7B2B

Solution structure of the Pax NRPS docking domain PaxB NDD

Authors

Watzel, J., Sarawi, S., Duchardt-Ferner, E., Bode, H.B., Woehnert, J.

Assembly

Peptide synthetase XpsB (Modular protein) (E.C.2.7.7.58,5.1.1.12)

Entity

1. Peptide synthetase XpsB (Modular protein) (E.C.2.7.7.58,5.1.1.12) (polymer, Thiol state: not present), 31 monomers, 3609.163 Da Detail

MNNNELTSLP LAERKRLLEL AKAAKLSRQH Y

Formula weight

3609.163 Da

Source organism

Xenorhabdus cabanillasii JM26

Exptl. method

solution NMR

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 90.1 %, Completeness (bb): 96.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	90.1 % (345 of 383)	90.1 % (182 of 202)	93.1 % (134 of 144)	78.4 % (29 of 37)
Backbone	96.7 % (178 of 184)	96.7 % (59 of 61)	96.8 % (90 of 93)	96.7 % (29 of 30)
Sidechain	86.1 % (198 of 230)	87.2 % (123 of 141)	91.5 % (75 of 82)	0.0 % (0 of 7)
Aromatic	0.0 % (0 of 12)	0.0 % (0 of 6)	0.0 % (0 of 6)
Methyl	100.0 % (38 of 38)	100.0 % (19 of 19)	100.0 % (19 of 19)

1. entity 1

MNNNELTSLP LAERKRLLEL AKAAKLSRQH Y

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5, Details 300 uM [U-15N] PaxB NDD, 50 mM sodium phosphate, 100 mM sodium chloride, 5 % [U-2H] D2O, 100 uM DSS, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	PaxB NDD	[U-15N]	300 uM
2	sodium phosphate	natural abundance	50 mM
3	sodium chloride	natural abundance	100 mM
4	D2O	[U-2H]	5 %
5	DSS	natural abundance	100 uM

Sample #2

#	Name	Isotope labeling	Concentration
6	PaxB NDD	[U-15N]	300 uM
7	sodium phosphate	natural abundance	50 mM
8	sodium chloride	natural abundance	100 mM
9	D2O	[U-2H]	5 %
10	DSS	natural abundance	100 uM

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5, Details 300 uM [U-10% 13C; U-15N] PaxB NDD, 50 mM sodium phosphate, 100 mM sodium chloride, 5 % [U-2H] D2O, 100 uM DSS, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
11	PaxB NDD	[U-10% 13C; U-15N]	300 uM
12	sodium phosphate	natural abundance	50 mM
13	sodium chloride	natural abundance	100 mM
14	D2O	[U-2H]	5 %
15	DSS	natural abundance	100 uM

Release date

2021-02-02

Citation

NMR resonance assignments for a docking domain pair with an attached thiolation domain from the PAX peptide-producing NRPS from Xenorhabdus cabanillasii
Watzel, J., Sarawi, S., Duchardt-Ferner, E., Bode, H.B., Woehnert, J.
Biomol. NMR Assign. (2021), 15, 229-234, PubMed 33675014 , DOI 10.1007/s12104-021-10010-1 , Abstract

Entries sharing articles BMRB: 2 entries Detail

  BMRB: 34575 released on 2021-02-02
    Title Solution structure of a non-covalent extended docking domain complex of the Pax NRPS: PaxA T1-CDD/PaxB NDD
  BMRB: 50594 released on 2020-11-24
    Title NMR resonance assignments for a docking domain pair with an attached thiolation domain from the PAX peptide-producing NRPS from Xenorhabdus cabanillasii

Related entities 1. Peptide synthetase XpsB (Modular protein) (E.C.2.7.7.58,5.1.1.12), : 1 : 1 : 2 entities Detail

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AVANCE III HD - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5, Details 300 uM [U-15N] PaxB NDD, 50 mM sodium phosphate, 100 mM sodium chloride, 5 % [U-2H] D2O, 100 uM DSS, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
6	PaxB NDD	[U-15N]	300 uM
7	sodium phosphate	natural abundance	50 mM
8	sodium chloride	natural abundance	100 mM
9	D2O	[U-2H]	5 %
10	DSS	natural abundance	100 uM

2 3D HNCO

Instrument

Bruker AVANCE III HD - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
6	PaxB NDD	[U-15N]	300 uM
7	sodium phosphate	natural abundance	50 mM
8	sodium chloride	natural abundance	100 mM
9	D2O	[U-2H]	5 %
10	DSS	natural abundance	100 uM

3 3D 1H-15N NOESY

Instrument

Bruker AVANCE II - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	PaxB NDD	[U-15N]	300 uM
2	sodium phosphate	natural abundance	50 mM
3	sodium chloride	natural abundance	100 mM
4	D2O	[U-2H]	5 %
5	DSS	natural abundance	100 uM

4 3D 1H-13C NOESY aliphatic

Instrument

Bruker AVANCE II - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
6	PaxB NDD	[U-15N]	300 uM
7	sodium phosphate	natural abundance	50 mM
8	sodium chloride	natural abundance	100 mM
9	D2O	[U-2H]	5 %
10	DSS	natural abundance	100 uM

5 2D 1H-13C HSQC aliphatic

Instrument

Bruker AVANCE III HD - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5, Details 300 uM [U-10% 13C; U-15N] PaxB NDD, 50 mM sodium phosphate, 100 mM sodium chloride, 5 % [U-2H] D2O, 100 uM DSS, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
11	PaxB NDD	[U-10% 13C; U-15N]	300 uM
12	sodium phosphate	natural abundance	50 mM
13	sodium chloride	natural abundance	100 mM
14	D2O	[U-2H]	5 %
15	DSS	natural abundance	100 uM

6 3D HBHA(CO)NH

Instrument

Bruker AVANCE III HD - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
6	PaxB NDD	[U-15N]	300 uM
7	sodium phosphate	natural abundance	50 mM
8	sodium chloride	natural abundance	100 mM
9	D2O	[U-2H]	5 %
10	DSS	natural abundance	100 uM

7 3D HNCACB

Instrument

Bruker AVANCE III HD - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
6	PaxB NDD	[U-15N]	300 uM
7	sodium phosphate	natural abundance	50 mM
8	sodium chloride	natural abundance	100 mM
9	D2O	[U-2H]	5 %
10	DSS	natural abundance	100 uM

8 2D 1H-13C HSQC aliphatic

Instrument

Bruker AVANCE II - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
6	PaxB NDD	[U-15N]	300 uM
7	sodium phosphate	natural abundance	50 mM
8	sodium chloride	natural abundance	100 mM
9	D2O	[U-2H]	5 %
10	DSS	natural abundance	100 uM

9 3D H(CCO)NH

Instrument

Bruker AVANCE II - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
6	PaxB NDD	[U-15N]	300 uM
7	sodium phosphate	natural abundance	50 mM
8	sodium chloride	natural abundance	100 mM
9	D2O	[U-2H]	5 %
10	DSS	natural abundance	100 uM

10 3D C(CO)NH

Instrument

Bruker AVANCE II - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
6	PaxB NDD	[U-15N]	300 uM
7	sodium phosphate	natural abundance	50 mM
8	sodium chloride	natural abundance	100 mM
9	D2O	[U-2H]	5 %
10	DSS	natural abundance	100 uM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34576_3.str
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	OK

Disulfide bonds

None

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

None

Non-standard residues

None

Content subtype: bmr34576_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	OK	382		100.0 (chain: 1, length: 31)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 31, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 220
  - ¹³C chemical shifts: 134
  - ¹⁵N chemical shifts: 28
- Completeness of assignments
  - Entity_assemble_ID: 1
- Peptide bond of PRO
- 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: 1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	202	182	90.1
¹³C chemical shifts	144	134	93.1
¹⁵N chemical shifts	37	28	75.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	61	59	96.7
¹³C chemical shifts	62	59	95.2
¹⁵N chemical shifts	30	28	93.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	141	123	87.2
¹³C chemical shifts	82	75	91.5
¹⁵N chemical shifts	7	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	20	19	95.0
¹³C chemical shifts	20	19	95.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	6	0	0.0
¹³C chemical shifts	6	0	0.0

Keywords PROTEIN, PROTEIN BINDING

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Found 1 Document (0.45 seconds)

BMRB: 34576

Sample #1

Sample #2

Sample #3

Entries sharing articles BMRB: 2 entries Detail

Related entities 1. Peptide synthetase XpsB (Modular protein) (E.C.2.7.7.58,5.1.1.12), : 1 : 1 : 2 entities Detail

Experiments performed 10 experiments Detail

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Chemical shift validation 3 contents Detail