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Found 1 Document (0.661 seconds)

BMRB: 34193

6EWS

Solution Structure of Rhabdopeptide NRPS Docking Domain Kj12A-NDD

Authors

Hacker, C., Cai, X., Kegler, C., Zhao, L., Weickhmann, A.K., Bode, H.B., Woehnert, J.

Assembly

Nonribosomal peptide synthetase StoA

Entity

1. Nonribosomal peptide synthetase StoA (polymer, Thiol state: not present), 63 monomers, 7490.197 Da Detail

MKNAAQIVDE ALNQGITLFV ADNRLQYETS RDNIPEELLN EWKYYRQDLI DFLQQLDAKE ETQ

Formula weight

7490.197 Da

Source organism

Xenorhabdus stockiae

Exptl. method

solution NMR

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 98.4 %, Completeness: 91.5 %, Completeness (bb): 94.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	91.5 % (704 of 769)	88.8 % (358 of 403)	94.2 % (274 of 291)	96.0 % (72 of 75)
Backbone	94.4 % (355 of 376)	92.9 % (117 of 126)	94.7 % (178 of 188)	96.8 % (60 of 62)
Sidechain	89.7 % (408 of 455)	87.0 % (241 of 277)	93.9 % (155 of 165)	92.3 % (12 of 13)
Aromatic	91.1 % (51 of 56)	85.7 % (24 of 28)	96.3 % (26 of 27)	100.0 % (1 of 1)
Methyl	100.0 % (72 of 72)	100.0 % (36 of 36)	100.0 % (36 of 36)

1. entity 1

MKNAAQIVDE ALNQGITLFV ADNRLQYETS RDNIPEELLN EWKYYRQDLI DFLQQLDAKE ETQ

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 293 K, pH 6.5, Details 1 mM [U-13C; U-15N] Kj12A NDD, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	Kj12A NDD	[U-13C; U-15N]	1 mM
2	sodium phosphate buffer	natural abundance	50 mM
3	sodium chloride	natural abundance	100 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 293 K, pH 6.5, Details 500 uM [U-15N] Kj12A NDD, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	Kj12A NDD	[U-15N]	500 uM
5	sodium phosphate buffer	natural abundance	50 mM
6	sodium chloride	natural abundance	100 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: -0.15 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: -0.15 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: -0.05 ppm, Outliers: 3 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: 0.08 ppm, Outliers: 1 Detail

Release date

2018-04-04

Citation

Structure-based redesign of docking domain interactions modulates the product spectrum of a rhabdopeptide-synthesizing NRPS
Hacker, C., Cai, X., Kegler, C., Zhao, L., Weickhmann, A.K., Bode, H.B., Woehnert, J.
Nat. Commun. (2018), 9, 4366-4366, PubMed 30341296 , DOI 10.1038/s41467-018-06712-1 , Abstract

Entries sharing articles BMRB: 3 entries Detail

  BMRB: 34194 released on 2018-04-04
    Title Solution Structure of Rhabdopeptide NRPS Docking Domain Kj12B-NDD
  BMRB: 34195 released on 2018-04-04
    Title Solution Structure of Rhabdopeptide NRPS Docking Domain Kj12C-NDD
  BMRB: 34196 released on 2018-04-04
    Title Solution Structure of Docking Domain Complex of RXP NRPS: Kj12C NDD - Kj12B CDD

Related entities 1. Nonribosomal peptide synthetase StoA, : 3 entities Detail

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 293 K, pH 6.5, Details 500 uM [U-15N] Kj12A NDD, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	Kj12A NDD	[U-15N]	500 uM
5	sodium phosphate buffer	natural abundance	50 mM
6	sodium chloride	natural abundance	100 mM

2 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 293 K, pH 6.5, Details 1 mM [U-13C; U-15N] Kj12A NDD, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	Kj12A NDD	[U-13C; U-15N]	1 mM
2	sodium phosphate buffer	natural abundance	50 mM
3	sodium chloride	natural abundance	100 mM

3 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 293 K, pH 6.5, Details 1 mM [U-13C; U-15N] Kj12A NDD, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	Kj12A NDD	[U-13C; U-15N]	1 mM
2	sodium phosphate buffer	natural abundance	50 mM
3	sodium chloride	natural abundance	100 mM

4 3D HN(CA)CO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 293 K, pH 6.5, Details 1 mM [U-13C; U-15N] Kj12A NDD, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	Kj12A NDD	[U-13C; U-15N]	1 mM
2	sodium phosphate buffer	natural abundance	50 mM
3	sodium chloride	natural abundance	100 mM

5 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 293 K, pH 6.5, Details 1 mM [U-13C; U-15N] Kj12A NDD, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	Kj12A NDD	[U-13C; U-15N]	1 mM
2	sodium phosphate buffer	natural abundance	50 mM
3	sodium chloride	natural abundance	100 mM

6 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - na MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 293 K, pH 6.5, Details 1 mM [U-13C; U-15N] Kj12A NDD, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	Kj12A NDD	[U-13C; U-15N]	1 mM
2	sodium phosphate buffer	natural abundance	50 mM
3	sodium chloride	natural abundance	100 mM

7 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 950 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 293 K, pH 6.5, Details 1 mM [U-13C; U-15N] Kj12A NDD, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	Kj12A NDD	[U-13C; U-15N]	1 mM
2	sodium phosphate buffer	natural abundance	50 mM
3	sodium chloride	natural abundance	100 mM

8 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 950 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 293 K, pH 6.5, Details 1 mM [U-13C; U-15N] Kj12A NDD, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	Kj12A NDD	[U-13C; U-15N]	1 mM
2	sodium phosphate buffer	natural abundance	50 mM
3	sodium chloride	natural abundance	100 mM

9 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 293 K, pH 6.5, Details 500 uM [U-15N] Kj12A NDD, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	Kj12A NDD	[U-15N]	500 uM
5	sodium phosphate buffer	natural abundance	50 mM
6	sodium chloride	natural abundance	100 mM

10 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 293 K, pH 6.5, Details 1 mM [U-13C; U-15N] Kj12A NDD, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	Kj12A NDD	[U-13C; U-15N]	1 mM
2	sodium phosphate buffer	natural abundance	50 mM
3	sodium chloride	natural abundance	100 mM

11 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - na MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 293 K, pH 6.5, Details 1 mM [U-13C; U-15N] Kj12A NDD, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	Kj12A NDD	[U-13C; U-15N]	1 mM
2	sodium phosphate buffer	natural abundance	50 mM
3	sodium chloride	natural abundance	100 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_34193_6ews.nef
Input source #2: Coordindates	6ews.cif
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	Warning

Disulfide bonds

None

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---
MKNAAQIVDEALNQGITLFVADNRLQYETSRDNIPEELLNEWKYYRQDLIDFLQQLDAKEETQ
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MKNAAQIVDEALNQGITLFVADNRLQYETSRDNIPEELLNEWKYYRQDLIDFLQQLDAKEETQ

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	63	0	0	100.0

Content subtype: combined_34193_6ews.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	737		98.4 (chain: A, length: 63)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	2005 (1)	noe	98.4 (chain: A, length: 63)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	102 (102)	.	90.5 (chain: A, length: 63)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 63, Sequence coverage: 98.4%
- Total number of assignments
  - ¹H chemical shifts: 383
  - ¹³C chemical shifts: 282
  - ¹⁵N chemical shifts: 72
- Completeness of assignments
  - Entity_assemble_ID: A
- 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: A

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	403	383	95.0
¹³C chemical shifts	291	282	96.9
¹⁵N chemical shifts	78	72	92.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	126	122	96.8
¹³C chemical shifts	126	122	96.8
¹⁵N chemical shifts	62	60	96.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	277	261	94.2
¹³C chemical shifts	165	160	97.0
¹⁵N chemical shifts	16	12	75.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	37	36	97.3
¹³C chemical shifts	37	36	97.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	28	28	100.0
¹³C chemical shifts	27	27	100.0
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 63, Sequence coverage: 98.4%
- Total number of restraints: 1997
- Weight of restraints: 1.0 (1997)
- Potential type of restraints: upper-bound-parabolic (1997)
- Range of distance target values: 2.44, 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

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 63, Sequence coverage: 90.5%
- Total number of restraints: 102
- Total number of restraints per polymer type: 102
- Weight of restraints: 1.0 (102)
- Potential type of restraints: square-well-parabolic (102)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords PEPTIDE BINDING PROTEIN, PROTEIN

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Found 1 Document (0.661 seconds)

BMRB: 34193

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles BMRB: 3 entries Detail

Related entities 1. Nonribosomal peptide synthetase StoA, : 3 entities Detail

Experiments performed 11 experiments Detail

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NMR combined restraints 4 contents Detail