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Found 1 Document (0.426 seconds)

BMRB: 34195

6EWU

Solution Structure of Rhabdopeptide NRPS Docking Domain Kj12C-NDD

Authors

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

Assembly

Nonribosomal peptide synthetase StoC

Entity

1. Nonribosomal peptide synthetase StoC (polymer, Thiol state: not present), 63 monomers, 7315.032 Da Detail

GIDAAQIVDE ALEQGITLFV VNNRLQYETS RDSIPTELLN KWKQHKQELI DFLNQLDSEE QTK

Formula weight

7315.032 Da

Source organism

Xenorhabdus stockiae

Exptl. method

NMR

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 95.3 %, Completeness (bb): 95.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	95.3 % (725 of 761)	95.7 % (381 of 398)	94.1 % (272 of 289)	97.3 % (72 of 74)
Backbone	95.7 % (360 of 376)	97.6 % (124 of 127)	94.1 % (176 of 187)	96.8 % (60 of 62)
Sidechain	95.1 % (424 of 446)	94.8 % (257 of 271)	95.1 % (155 of 163)	100.0 % (12 of 12)
Aromatic	81.8 % (36 of 44)	81.8 % (18 of 22)	81.0 % (17 of 21)	100.0 % (1 of 1)
Methyl	97.4 % (76 of 78)	97.4 % (38 of 39)	97.4 % (38 of 39)

1. entity 1

GIDAAQIVDE ALEQGITLFV VNNRLQYETS RDSIPTELLN KWKQHKQELI DFLNQLDSEE QTK

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 293 K, pH 6.5, Details 200 uM [U-15N] Kj12CDD, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	Kj12CDD	[U-15N]	200 uM
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 700 uM [U-13C; U-15N] Kj12CDD, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	Kj12CDD	[U-13C; U-15N]	700 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: -0.05 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: -0.05 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: -0.05 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: 0.0 ppm, Outliers: 3 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

Related entities 1. Nonribosomal peptide synthetase StoC, : 9 entities Detail

Experiments performed 14 experiments Detail

1 3D 1H-15N NOESY

Instrument

Bruker Avance - na MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 293 K, pH 6.5, Details 200 uM [U-15N] Kj12CDD, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	Kj12CDD	[U-15N]	200 uM
2	sodium phosphate buffer	natural abundance	50 mM
3	sodium chloride	natural abundance	100 mM

2 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - na MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 293 K, pH 6.5, Details 700 uM [U-13C; U-15N] Kj12CDD, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	Kj12CDD	[U-13C; U-15N]	700 uM
5	sodium phosphate buffer	natural abundance	50 mM
6	sodium chloride	natural abundance	100 mM

3 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 700 uM [U-13C; U-15N] Kj12CDD, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	Kj12CDD	[U-13C; U-15N]	700 uM
5	sodium phosphate buffer	natural abundance	50 mM
6	sodium chloride	natural abundance	100 mM

4 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 700 uM [U-13C; U-15N] Kj12CDD, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	Kj12CDD	[U-13C; U-15N]	700 uM
5	sodium phosphate buffer	natural abundance	50 mM
6	sodium chloride	natural abundance	100 mM

5 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 700 uM [U-13C; U-15N] Kj12CDD, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	Kj12CDD	[U-13C; U-15N]	700 uM
5	sodium phosphate buffer	natural abundance	50 mM
6	sodium chloride	natural abundance	100 mM

6 2D 1H-15N HSQC

Instrument

Bruker Avance - na MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 293 K, pH 6.5, Details 200 uM [U-15N] Kj12CDD, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	Kj12CDD	[U-15N]	200 uM
2	sodium phosphate buffer	natural abundance	50 mM
3	sodium chloride	natural abundance	100 mM

7 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 700 uM [U-13C; U-15N] Kj12CDD, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	Kj12CDD	[U-13C; U-15N]	700 uM
5	sodium phosphate buffer	natural abundance	50 mM
6	sodium chloride	natural abundance	100 mM

8 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - na MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 293 K, pH 6.5, Details 700 uM [U-13C; U-15N] Kj12CDD, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	Kj12CDD	[U-13C; U-15N]	700 uM
5	sodium phosphate buffer	natural abundance	50 mM
6	sodium chloride	natural abundance	100 mM

9 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz Wasserwerk

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 293 K, pH 6.5, Details 700 uM [U-13C; U-15N] Kj12CDD, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	Kj12CDD	[U-13C; U-15N]	700 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 Wasserwerk

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 293 K, pH 6.5, Details 700 uM [U-13C; U-15N] Kj12CDD, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	Kj12CDD	[U-13C; U-15N]	700 uM
5	sodium phosphate buffer	natural abundance	50 mM
6	sodium chloride	natural abundance	100 mM

11 3D (H)C(CCO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 293 K, pH 6.5, Details 700 uM [U-13C; U-15N] Kj12CDD, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	Kj12CDD	[U-13C; U-15N]	700 uM
5	sodium phosphate buffer	natural abundance	50 mM
6	sodium chloride	natural abundance	100 mM

12 3D H(CCO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 293 K, pH 6.5, Details 700 uM [U-13C; U-15N] Kj12CDD, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	Kj12CDD	[U-13C; U-15N]	700 uM
5	sodium phosphate buffer	natural abundance	50 mM
6	sodium chloride	natural abundance	100 mM

13 3D HBHA(CO)NH

Instrument

Bruker Avance - na MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 293 K, pH 6.5, Details 700 uM [U-13C; U-15N] Kj12CDD, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	Kj12CDD	[U-13C; U-15N]	700 uM
5	sodium phosphate buffer	natural abundance	50 mM
6	sodium chloride	natural abundance	100 mM

14 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 700 uM [U-13C; U-15N] Kj12CDD, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	Kj12CDD	[U-13C; U-15N]	700 uM
5	sodium phosphate buffer	natural abundance	50 mM
6	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_34195_6ewu.nef
Input source #2: Coordindates	6ewu.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---
GIDAAQIVDEALEQGITLFVVNNRLQYETSRDSIPTELLNKWKQHKQELIDFLNQLDSEEQTK
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GIDAAQIVDEALEQGITLFVVNNRLQYETSRDSIPTELLNKWKQHKQELIDFLNQLDSEEQTK

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_34195_6ewu.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	731		100.0 (chain: A, length: 63)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	1971 (1)	noe	100.0 (chain: A, length: 63)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	106 (106)	.	92.1 (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: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 385
  - ¹³C chemical shifts: 274
  - ¹⁵N chemical shifts: 72
- 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	398	385	96.7
¹³C chemical shifts	289	274	94.8
¹⁵N chemical shifts	76	72	94.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	127	126	99.2
¹³C chemical shifts	126	119	94.4
¹⁵N chemical shifts	62	60	96.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	271	259	95.6
¹³C chemical shifts	163	155	95.1
¹⁵N chemical shifts	14	12	85.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	39	38	97.4
¹³C chemical shifts	39	38	97.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	22	16	72.7
¹³C chemical shifts	21	15	71.4
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: 63, Sequence coverage: 100.0%
- Total number of restraints: 1959
- Weight of restraints: 1.0 (1959)
- Potential type of restraints: upper-bound-parabolic (1959)
- Range of distance target values: 2.34, 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: 92.1%
- Total number of restraints: 106
- Total number of restraints per polymer type: 106
- Weight of restraints: 1.0 (106)
- Potential type of restraints: square-well-parabolic (106)
- 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 (0.426 seconds)

BMRB: 34195

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Nonribosomal peptide synthetase StoC, : 9 entities Detail

Experiments performed 14 experiments Detail

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NMR combined restraints 4 contents Detail