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BMRB: 34194

6EWT

Solution Structure of Rhabdopeptide NRPS Docking Domain Kj12B-NDD

Authors

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

Assembly

Nonribosomal peptide synthetase StoB

Entity

1. Nonribosomal peptide synthetase StoB (polymer, Thiol state: not present), 62 monomers, 7236.037 Da Detail

MKNAAKIVNE ALNQGITLFV SDNKLKYKTN RDSIPSELLE EWKQHKQELI DFLTQLESEE ES

Formula weight

7236.037 Da

Source organism

Xenorhabdus stockiae

Exptl. method

solution NMR

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 98.3 %, Completeness (bb): 98.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	98.3 % (748 of 761)	97.3 % (390 of 401)	99.7 % (288 of 289)	98.6 % (70 of 71)
Backbone	98.9 % (366 of 370)	97.6 % (121 of 124)	100.0 % (185 of 185)	98.4 % (60 of 61)
Sidechain	98.0 % (443 of 452)	97.1 % (269 of 277)	99.4 % (164 of 165)	100.0 % (10 of 10)
Aromatic	100.0 % (44 of 44)	100.0 % (22 of 22)	100.0 % (21 of 21)	100.0 % (1 of 1)
Methyl	97.1 % (66 of 68)	94.1 % (32 of 34)	100.0 % (34 of 34)

1. entity 1

MKNAAKIVNE ALNQGITLFV SDNKLKYKTN RDSIPSELLE EWKQHKQELI DFLTQLESEE ES

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 bar, Temperature 293 K, pH 6.5, Details 1 mM [U-13C; U-15N] Kj12BCDD, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	Kj12BCDD	[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 bar, Temperature 293 K, pH 6.5, Details 200 uM [U-15N] Kj12BCDD, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	Kj12BCDD	[U-15N]	200 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: -0.02 ppm, Outliers: 2 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: -0.02 ppm, Outliers: 2 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: 0.04 ppm, Outliers: 2 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: 3.89 ppm, Outliers: 4 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: 34193 released on 2018-04-04
    Title Solution Structure of Rhabdopeptide NRPS Docking Domain Kj12A-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 StoB, : 1 : 11 entities Detail

Experiments performed 12 experiments Detail

1 3D HNCACB

Instrument

Bruker Avance - na MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 bar, Temperature 293 K, pH 6.5, Details 1 mM [U-13C; U-15N] Kj12BCDD, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	Kj12BCDD	[U-13C; U-15N]	1 mM
2	sodium phosphate buffer	natural abundance	50 mM
3	sodium chloride	natural abundance	100 mM

2 3D HNCO

Instrument

Bruker Avance - na MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 bar, Temperature 293 K, pH 6.5, Details 1 mM [U-13C; U-15N] Kj12BCDD, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	Kj12BCDD	[U-13C; U-15N]	1 mM
2	sodium phosphate buffer	natural abundance	50 mM
3	sodium chloride	natural abundance	100 mM

3 3D HN(CA)CO

Instrument

Bruker Avance - na MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 bar, Temperature 293 K, pH 6.5, Details 1 mM [U-13C; U-15N] Kj12BCDD, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	Kj12BCDD	[U-13C; U-15N]	1 mM
2	sodium phosphate buffer	natural abundance	50 mM
3	sodium chloride	natural abundance	100 mM

4 3D H(CCO)NH

Instrument

Bruker Avance - na MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 bar, Temperature 293 K, pH 6.5, Details 1 mM [U-13C; U-15N] Kj12BCDD, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	Kj12BCDD	[U-13C; U-15N]	1 mM
2	sodium phosphate buffer	natural abundance	50 mM
3	sodium chloride	natural abundance	100 mM

5 3D C(CO)NH

Instrument

Bruker Avance - na MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 bar, Temperature 293 K, pH 6.5, Details 1 mM [U-13C; U-15N] Kj12BCDD, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	Kj12BCDD	[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

Instrument

Bruker Avance - na MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 bar, Temperature 293 K, pH 6.5, Details 1 mM [U-13C; U-15N] Kj12BCDD, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	Kj12BCDD	[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

Instrument

Bruker Avance - na MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 bar, Temperature 293 K, pH 6.5, Details 1 mM [U-13C; U-15N] Kj12BCDD, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	Kj12BCDD	[U-13C; U-15N]	1 mM
2	sodium phosphate buffer	natural abundance	50 mM
3	sodium chloride	natural abundance	100 mM

8 3D 1H-15N NOESY-HSQC

Instrument

Bruker Avance - na MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 bar, Temperature 293 K, pH 6.5, Details 200 uM [U-15N] Kj12BCDD, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	Kj12BCDD	[U-15N]	200 uM
5	sodium phosphate buffer	natural abundance	50 mM
6	sodium chloride	natural abundance	100 mM

9 2D 1H-15N HSQC

Instrument

Bruker Avance - na MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 bar, Temperature 293 K, pH 6.5, Details 200 uM [U-15N] Kj12BCDD, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	Kj12BCDD	[U-15N]	200 uM
5	sodium phosphate buffer	natural abundance	50 mM
6	sodium chloride	natural abundance	100 mM

10 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz WW

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 bar, Temperature 293 K, pH 6.5, Details 1 mM [U-13C; U-15N] Kj12BCDD, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	Kj12BCDD	[U-13C; U-15N]	1 mM
2	sodium phosphate buffer	natural abundance	50 mM
3	sodium chloride	natural abundance	100 mM

11 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz WW

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 bar, Temperature 293 K, pH 6.5, Details 1 mM [U-13C; U-15N] Kj12BCDD, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	Kj12BCDD	[U-13C; U-15N]	1 mM
2	sodium phosphate buffer	natural abundance	50 mM
3	sodium chloride	natural abundance	100 mM

12 3D HBHA(CO)NH

Instrument

Bruker Avance - na MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 bar, Temperature 293 K, pH 6.5, Details 1 mM [U-13C; U-15N] Kj12BCDD, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	Kj12BCDD	[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_34194_6ewt.nef
Input source #2: Coordindates	6ewt.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--
MKNAAKIVNEALNQGITLFVSDNKLKYKTNRDSIPSELLEEWKQHKQELIDFLTQLESEEES
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MKNAAKIVNEALNQGITLFVSDNKLKYKTNRDSIPSELLEEWKQHKQELIDFLTQLESEEES

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	62	0	0	100.0

Content subtype: combined_34194_6ewt.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	755		100.0 (chain: A, length: 62)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	2224 (1)	noe	100.0 (chain: A, length: 62)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	96 (96)	.	88.7 (chain: A, length: 62)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 62, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 397
  - ¹³C chemical shifts: 288
  - ¹⁵N chemical shifts: 70
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	401	397	99.0
¹³C chemical shifts	289	288	99.7
¹⁵N chemical shifts	72	70	97.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	124	123	99.2
¹³C chemical shifts	124	124	100.0
¹⁵N chemical shifts	61	60	98.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	277	274	98.9
¹³C chemical shifts	165	164	99.4
¹⁵N chemical shifts	11	10	90.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	35	34	97.1
¹³C chemical shifts	35	34	97.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	22	22	100.0
¹³C chemical shifts	21	21	100.0
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 62, Sequence coverage: 100.0%
- Total number of restraints: 2217
- Weight of restraints: 1.0 (2217)
- Potential type of restraints: upper-bound-parabolic (2217)
- Range of distance target values: 2.59, 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: 62, Sequence coverage: 88.7%
- Total number of restraints: 96
- Total number of restraints per polymer type: 96
- Weight of restraints: 1.0 (96)
- Potential type of restraints: square-well-parabolic (96)
- 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 (0.581 seconds)

BMRB: 34194

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 StoB, : 1 : 11 entities Detail

Experiments performed 12 experiments Detail

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NMR combined restraints 4 contents Detail