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Found 1 Document (0.509 seconds)

BMRB: 34196

6EWV

Solution Structure of Docking Domain Complex of RXP NRPS: Kj12C NDD - Kj12B CDD

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), 99 monomers, 11094.04 Da Detail

GIDAAQIVDE ALEQGITLFV VNNRLQYETS RDSIPTELLN KWKQHKQELI DFLNQLDSEE QTKGSGSGSG SGSGSLLKEK RKHFQAEQNS SQEYLRGEI

Formula weight

11094.04 Da

Source organism

Xenorhabdus stockiae

Exptl. method

solution NMR

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 93.9 %, Completeness: 84.2 %, Completeness (bb): 80.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	84.2 % (972 of 1154)	89.0 % (540 of 607)	77.6 % (336 of 433)	84.2 % (96 of 114)
Backbone	80.2 % (475 of 592)	89.8 % (185 of 206)	69.1 % (199 of 288)	92.9 % (91 of 98)
Sidechain	89.4 % (583 of 652)	88.5 % (355 of 401)	94.9 % (223 of 235)	31.3 % (5 of 16)
Aromatic	81.8 % (54 of 66)	81.8 % (27 of 33)	81.3 % (26 of 32)	100.0 % (1 of 1)
Methyl	100.0 % (96 of 96)	100.0 % (48 of 48)	100.0 % (48 of 48)

1. entity 1

GIDAAQIVDE ALEQGITLFV VNNRLQYETS RDSIPTELLN KWKQHKQELI DFLNQLDSEE QTKGSGSGSG SGSGSLLKEK RKHFQAEQNS SQEYLRGEI

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 293 K, pH 6.5, Details 700 uM [U-99% 15N] KJ12C Ndd 12xGS KJ12B Cdd, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	KJ12C Ndd 12xGS KJ12B Cdd	[U-99% 15N]	700 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 850 uM [U-99% 13C; U-99% 15N] KJ12C Ndd 12xGS KJ12B Cdd, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	KJ12C Ndd 12xGS KJ12B Cdd	[U-99% 13C; U-99% 15N]	850 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: -0.06 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: -0.06 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: -0.01 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
Cai, X., Hacker, C., Kegler, C., Zhai, L., Woehnert, J., Bode, H.B.
Nat. Commun. (2018), 9, 4366-4366, PubMed 30341296 , DOI 10.1038/s41467-018-06712-1 , Abstract

Related entities 1. Nonribosomal peptide synthetase StoC, : 2 entities Detail

Experiments performed 11 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 700 uM [U-99% 15N] KJ12C Ndd 12xGS KJ12B Cdd, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	KJ12C Ndd 12xGS KJ12B Cdd	[U-99% 15N]	700 uM
2	sodium phosphate buffer	natural abundance	50 mM
3	sodium chloride	natural abundance	100 mM

2 3D 1H-13C 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 850 uM [U-99% 13C; U-99% 15N] KJ12C Ndd 12xGS KJ12B Cdd, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	KJ12C Ndd 12xGS KJ12B Cdd	[U-99% 13C; U-99% 15N]	850 uM
5	sodium phosphate buffer	natural abundance	50 mM
6	sodium chloride	natural abundance	100 mM

3 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz ww

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 293 K, pH 6.5, Details 850 uM [U-99% 13C; U-99% 15N] KJ12C Ndd 12xGS KJ12B Cdd, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	KJ12C Ndd 12xGS KJ12B Cdd	[U-99% 13C; U-99% 15N]	850 uM
5	sodium phosphate buffer	natural abundance	50 mM
6	sodium chloride	natural abundance	100 mM

4 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 850 uM [U-99% 13C; U-99% 15N] KJ12C Ndd 12xGS KJ12B Cdd, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	KJ12C Ndd 12xGS KJ12B Cdd	[U-99% 13C; U-99% 15N]	850 uM
5	sodium phosphate buffer	natural abundance	50 mM
6	sodium chloride	natural abundance	100 mM

5 3D HBHA(CO)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 850 uM [U-99% 13C; U-99% 15N] KJ12C Ndd 12xGS KJ12B Cdd, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	KJ12C Ndd 12xGS KJ12B Cdd	[U-99% 13C; U-99% 15N]	850 uM
5	sodium phosphate buffer	natural abundance	50 mM
6	sodium chloride	natural abundance	100 mM

6 3D b-tr-HN(CO)CA

Instrument

Bruker Avance - na MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 293 K, pH 6.5, Details 850 uM [U-99% 13C; U-99% 15N] KJ12C Ndd 12xGS KJ12B Cdd, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	KJ12C Ndd 12xGS KJ12B Cdd	[U-99% 13C; U-99% 15N]	850 uM
5	sodium phosphate buffer	natural abundance	50 mM
6	sodium chloride	natural abundance	100 mM

7 3D b-tr-HNCACB

Instrument

Bruker Avance - na MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 293 K, pH 6.5, Details 850 uM [U-99% 13C; U-99% 15N] KJ12C Ndd 12xGS KJ12B Cdd, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	KJ12C Ndd 12xGS KJ12B Cdd	[U-99% 13C; U-99% 15N]	850 uM
5	sodium phosphate buffer	natural abundance	50 mM
6	sodium chloride	natural abundance	100 mM

8 3D b-tr-HNCO

Instrument

Bruker Avance - na MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 293 K, pH 6.5, Details 850 uM [U-99% 13C; U-99% 15N] KJ12C Ndd 12xGS KJ12B Cdd, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	KJ12C Ndd 12xGS KJ12B Cdd	[U-99% 13C; U-99% 15N]	850 uM
5	sodium phosphate buffer	natural abundance	50 mM
6	sodium chloride	natural abundance	100 mM

9 2D 1H-15N b-tr-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 700 uM [U-99% 15N] KJ12C Ndd 12xGS KJ12B Cdd, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	KJ12C Ndd 12xGS KJ12B Cdd	[U-99% 15N]	700 uM
2	sodium phosphate buffer	natural abundance	50 mM
3	sodium chloride	natural abundance	100 mM

10 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 293 K, pH 6.5, Details 850 uM [U-99% 13C; U-99% 15N] KJ12C Ndd 12xGS KJ12B Cdd, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	KJ12C Ndd 12xGS KJ12B Cdd	[U-99% 13C; U-99% 15N]	850 uM
5	sodium phosphate buffer	natural abundance	50 mM
6	sodium chloride	natural abundance	100 mM

11 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 293 K, pH 6.5, Details 850 uM [U-99% 13C; U-99% 15N] KJ12C Ndd 12xGS KJ12B Cdd, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	KJ12C Ndd 12xGS KJ12B Cdd	[U-99% 13C; U-99% 15N]	850 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_34196_6ewv.nef
Input source #2: Coordindates	6ewv.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--------70-------1550------1560--------
GIDAAQIVDEALEQGITLFVVNNRLQYETSRDSIPTELLNKWKQHKQELIDFLNQLDSEEQTKGSGSGSGSGSGSLLKEKRKHFQAEQNSSQEYLRGEI
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GIDAAQIVDEALEQGITLFVVNNRLQYETSRDSIPTELLNKWKQHKQELIDFLNQLDSEEQTKGSGSGSGSGSGSLLKEKRKHFQAEQNSSQEYLRGEI
--------10--------20--------30--------40--------50--------60--------70--------80--------90---------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	99	0	0	100.0

Content subtype: combined_34196_6ewv.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	932		91.9 (chain: A, length: 99)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	3096 (1)	noe	91.9 (chain: A, length: 99)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	140 (140)	.	78.8 (chain: A, length: 99)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 99, Sequence coverage: 91.9%
- Total number of assignments
  - ¹H chemical shifts: 530
  - ¹³C chemical shifts: 312
  - ¹⁵N chemical shifts: 90
- 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	607	530	87.3
¹³C chemical shifts	433	312	72.1
¹⁵N chemical shifts	118	90	76.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	206	183	88.8
¹³C chemical shifts	198	90	45.5
¹⁵N chemical shifts	98	89	90.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	401	347	86.5
¹³C chemical shifts	235	222	94.5
¹⁵N chemical shifts	20	1	5.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	48	48	100.0
¹³C chemical shifts	48	48	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	33	27	81.8
¹³C chemical shifts	32	26	81.2
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: 99, Sequence coverage: 91.9%
- Total number of restraints: 3096
- Weight of restraints: 1.0 (3096)
- Potential type of restraints: upper-bound-parabolic (3096)
- Range of distance target values: 2.39, 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: 99, Sequence coverage: 78.8%
- Total number of restraints: 140
- Total number of restraints per polymer type: 140
- Weight of restraints: 1.0 (140)
- Potential type of restraints: square-well-parabolic (140)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Docking Domains, PEPTIDE BINDING PROTEIN, PROTEIN, Rhabdopeptide, Solution Structure

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Found 1 Document (0.509 seconds)

BMRB: 34196

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Nonribosomal peptide synthetase StoC, : 2 entities Detail

Experiments performed 11 experiments Detail

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NMR combined restraints 4 contents Detail