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BMRB: 25706

2N5D

1H, 13C, and 15N Chemical Shift Assignments of PKS domains

Authors

Dorival, G., Annaval, T., Risser, F., Collin, S., Roblin, P., Jacob, C., Gruez, A., Chagot, B., Weissman, K.J.

Assembly

VirA VirFG fusion

Entity

1. VirA VirFG fusion (polymer, Thiol state: all free), 84 monomers, 8445.332 Da Detail

GPGSYTGAGE PSQADLDALL SAVRDNRLSI EQAVTLLTPR RGGGSGGGSM DAKEILTRFK DGGLDRAAAQ ALLAGRTPAA APRP

Formula weight

8445.332 Da

Source organism

Streptomyces virginiae

Exptl. method

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.6 %, Completeness: 94.0 %, Completeness (bb): 93.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	94.0 % (814 of 866)	92.4 % (415 of 449)	95.5 % (320 of 335)	96.3 % (79 of 82)
Backbone	93.3 % (459 of 492)	91.4 % (160 of 175)	93.7 % (224 of 239)	96.2 % (75 of 78)
Sidechain	95.5 % (425 of 445)	93.1 % (255 of 274)	99.4 % (166 of 167)	100.0 % (4 of 4)
Aromatic	100.0 % (18 of 18)	100.0 % (9 of 9)	100.0 % (9 of 9)
Methyl	100.0 % (94 of 94)	100.0 % (47 of 47)	100.0 % (47 of 47)

1. entity

GPGSYTGAGE PSQADLDALL SAVRDNRLSI EQAVTLLTPR RGGGSGGGSM DAKEILTRFK DGGLDRAAAQ ALLAGRTPAA APRP

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		100 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

LACS Plot; CA

Referencing offset: -0.19 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.19 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.05 ppm, Outliers: 3 Detail

LACS Plot; CO

Referencing offset: -0.25 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2N5D, Strand ID: A Detail

Release date

2016-03-20

Citation

Characterization of Intersubunit Communication in the Virginiamycin trans-Acyl Transferase Polyketide Synthase
Dorival, G., Annaval, T., Risser, F., Collin, S., Roblin, P., Jacob, C., Gruez, A., Chagot, B., Weissman, K.J.
J. Am. Chem. Soc. (2016), 138, 4155-4167, PubMed 26982529 , DOI 10.1021/jacs.5b13372 , Abstract

Related entities 1. VirA VirFG fusion, : 1 : 2 entities Detail

Experiments performed 9 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz Avance III with cryoprobe TCI

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		100 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz Avance III with cryoprobe TCI

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		100 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

3 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz Avance III with cryoprobe TCI

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		100 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

4 3D HNCACB

Instrument

Bruker Avance - 600 MHz Avance III with cryoprobe TCI

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		100 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

5 3D HNCO

Instrument

Bruker Avance - 600 MHz Avance III with cryoprobe TCI

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		100 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

6 3D H(CCO)NH

Instrument

Bruker Avance - 600 MHz Avance III with cryoprobe TCI

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		100 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

7 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz Avance III with cryoprobe TCI

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		100 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

8 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 600 MHz Avance III with cryoprobe TCI

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		100 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

9 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz Avance III with cryoprobe TCI

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		1 mM
2	sodium phosphate	natural abundance		100 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25706_2n5d.nef
Input source #2: Coordindates	2n5d.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--------80----
GPGSYTGAGEPSQADLDALLSAVRDNRLSIEQAVTLLTPRRGGGSGGGSMDAKEILTRFKDGGLDRAAAQALLAGRTPAAAPRP
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GPGSYTGAGEPSQADLDALLSAVRDNRLSIEQAVTLLTPRRGGGSGGGSMDAKEILTRFKDGGLDRAAAQALLAGRTPAAAPRP

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	84	0	0	100.0

Content subtype: combined_25706_2n5d.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	823		97.6 (chain: A, length: 84)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	1965 (1)	noe	89.3 (chain: A, length: 84)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	88 (88)	.	59.5 (chain: A, length: 84)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 84, Sequence coverage: 97.6%
- Total number of assignments
  - ¹H chemical shifts: 422
  - ¹³C chemical shifts: 321
  - ¹⁵N chemical shifts: 80
- 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

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 84, Sequence coverage: 89.3%
- Total number of restraints: 1956
- Weight of restraints: 1.0 (1956)
- Potential type of restraints: upper-bound-parabolic (1956)
- Range of distance target values: 2.57, 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: 84, Sequence coverage: 59.5%
- Total number of restraints: 88
- Total number of restraints per polymer type: 88
- Weight of restraints: 1.0 (88)
- Potential type of restraints: square-well-parabolic (88)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords docking domain, nmr, polyketide synthase