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BMRB: 25787

2N6Z

Solution structure of the salicylate-loaded ArCP from yersiniabactin synthetase

Authors

Goodrich, A.C., Harden, B.J., Frueh, D.P.

Assembly

salicylate-loaded ArCP from yersiniabactin synthetase

Entity

1. salicylate-loaded ArCP from yersiniabactin synthetase (polymer, Thiol state: not present), 80 monomers, 10060.24 Da Detail

DNRHAADYQQ LRERLIQELN LTPQQLHEES NLIQAGLDXI RLMRWLHWFR KNGYRLTLRE LYAAPTLAAW NQLMLSRSPE

Formula weight

10060.24 Da

Source organism

Yersinia pestis

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.5 %, Completeness: 87.6 %, Completeness (bb): 91.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	87.6 % (861 of 983)	87.6 % (454 of 518)	88.0 % (329 of 374)	85.7 % (78 of 91)
Backbone	91.7 % (429 of 468)	95.5 % (150 of 157)	86.8 % (204 of 235)	98.7 % (75 of 76)
Sidechain	85.6 % (507 of 592)	84.2 % (304 of 361)	92.6 % (200 of 216)	20.0 % (3 of 15)
Aromatic	87.8 % (72 of 82)	87.8 % (36 of 41)	86.8 % (33 of 38)	100.0 % (3 of 3)
Methyl	100.0 % (92 of 92)	100.0 % (46 of 46)	100.0 % (46 of 46)

1. entity

DNRHAADYQQ LRERLIQELN LTPQQLHEES NLIQAGLDXI RLMRWLHWFR KNGYRLTLRE LYAAPTLAAW NQLMLSRSPE

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Loaded-ArCP	[U-99% 15N]		0.3-0.4 mM
2	ACES	natural abundance		50 mM
3	TCEP	natural abundance		0.5 mM
4	sodium chloride	natural abundance		150 mM
5	magnesium chloride	natural abundance		1 mM
6	DSS	natural abundance		0.1 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
9	Loaded-ArCP	[U-99% 13C; U-99% 15N]		0.3-0.4 mM
10	ACES	natural abundance		50 mM
11	TCEP	natural abundance		0.5 mM
12	sodium chloride	natural abundance		150 mM
13	magnesium chloride	natural abundance		1 mM
14	DSS	natural abundance		0.1 mM
15	ATP	natural abundance		2 mM
16	sodium salicylate	natural abundance		2 mM
17	Adenylation domain YbtE	natural abundance		20-100 nM
18	H2O	natural abundance		90 %
19	D2O	natural abundance		10 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
20	Loaded-ArCP	[U-99% 13C; U-99% 15N]		0.3-0.4 mM
21	ACES	natural abundance		50 mM
22	TCEP	natural abundance		0.5 mM
23	sodium chloride	natural abundance		150 mM
24	magnesium chloride	natural abundance		1 mM
25	DSS	natural abundance		0.1 mM
26	ATP	natural abundance		2 mM
27	sodium salicylate	[U-100% 13C]		0.5 mM
28	Adenylation domain YbtE	natural abundance		20-100 nM
29	D2O	natural abundance		100 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2N6Z, Strand ID: A Detail

Release date

2016-07-27

Citation

Solution Structure of a Nonribosomal Peptide Synthetase Carrier Protein Loaded with Its Substrate Reveals Transient, Well-Defined Contacts
Goodrich, A.C., Harden, B.J., Frueh, D.P.
J. Am. Chem. Soc. (2015), 137, 12100-12109, PubMed 26334259 , DOI 10.1021/jacs.5b07772 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 25786 released on 2016-07-27
Title Solution structure of holo ArCP from yersiniabactin synthetase

Related entities 1. salicylate-loaded ArCP from yersiniabactin synthetase, : 1 : 1 : 1 : 29 entities Detail

Experiments performed 9 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Loaded-ArCP	[U-99% 15N]		0.3-0.4 mM
2	ACES	natural abundance		50 mM
3	TCEP	natural abundance		0.5 mM
4	sodium chloride	natural abundance		150 mM
5	magnesium chloride	natural abundance		1 mM
6	DSS	natural abundance		0.1 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

2 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
9	Loaded-ArCP	[U-99% 13C; U-99% 15N]		0.3-0.4 mM
10	ACES	natural abundance		50 mM
11	TCEP	natural abundance		0.5 mM
12	sodium chloride	natural abundance		150 mM
13	magnesium chloride	natural abundance		1 mM
14	DSS	natural abundance		0.1 mM
15	ATP	natural abundance		2 mM
16	sodium salicylate	natural abundance		2 mM
17	Adenylation domain YbtE	natural abundance		20-100 nM
18	H2O	natural abundance		90 %
19	D2O	natural abundance		10 %

3 3D HNCA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
9	Loaded-ArCP	[U-99% 13C; U-99% 15N]		0.3-0.4 mM
10	ACES	natural abundance		50 mM
11	TCEP	natural abundance		0.5 mM
12	sodium chloride	natural abundance		150 mM
13	magnesium chloride	natural abundance		1 mM
14	DSS	natural abundance		0.1 mM
15	ATP	natural abundance		2 mM
16	sodium salicylate	natural abundance		2 mM
17	Adenylation domain YbtE	natural abundance		20-100 nM
18	H2O	natural abundance		90 %
19	D2O	natural abundance		10 %

4 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
9	Loaded-ArCP	[U-99% 13C; U-99% 15N]		0.3-0.4 mM
10	ACES	natural abundance		50 mM
11	TCEP	natural abundance		0.5 mM
12	sodium chloride	natural abundance		150 mM
13	magnesium chloride	natural abundance		1 mM
14	DSS	natural abundance		0.1 mM
15	ATP	natural abundance		2 mM
16	sodium salicylate	natural abundance		2 mM
17	Adenylation domain YbtE	natural abundance		20-100 nM
18	H2O	natural abundance		90 %
19	D2O	natural abundance		10 %

5 3D H(CCO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
9	Loaded-ArCP	[U-99% 13C; U-99% 15N]		0.3-0.4 mM
10	ACES	natural abundance		50 mM
11	TCEP	natural abundance		0.5 mM
12	sodium chloride	natural abundance		150 mM
13	magnesium chloride	natural abundance		1 mM
14	DSS	natural abundance		0.1 mM
15	ATP	natural abundance		2 mM
16	sodium salicylate	natural abundance		2 mM
17	Adenylation domain YbtE	natural abundance		20-100 nM
18	H2O	natural abundance		90 %
19	D2O	natural abundance		10 %

6 3D HN(CA)CO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
9	Loaded-ArCP	[U-99% 13C; U-99% 15N]		0.3-0.4 mM
10	ACES	natural abundance		50 mM
11	TCEP	natural abundance		0.5 mM
12	sodium chloride	natural abundance		150 mM
13	magnesium chloride	natural abundance		1 mM
14	DSS	natural abundance		0.1 mM
15	ATP	natural abundance		2 mM
16	sodium salicylate	natural abundance		2 mM
17	Adenylation domain YbtE	natural abundance		20-100 nM
18	H2O	natural abundance		90 %
19	D2O	natural abundance		10 %

7 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Loaded-ArCP	[U-99% 15N]		0.3-0.4 mM
2	ACES	natural abundance		50 mM
3	TCEP	natural abundance		0.5 mM
4	sodium chloride	natural abundance		150 mM
5	magnesium chloride	natural abundance		1 mM
6	DSS	natural abundance		0.1 mM
7	H2O	natural abundance		90 %
8	D2O	natural abundance		10 %

8 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
9	Loaded-ArCP	[U-99% 13C; U-99% 15N]		0.3-0.4 mM
10	ACES	natural abundance		50 mM
11	TCEP	natural abundance		0.5 mM
12	sodium chloride	natural abundance		150 mM
13	magnesium chloride	natural abundance		1 mM
14	DSS	natural abundance		0.1 mM
15	ATP	natural abundance		2 mM
16	sodium salicylate	natural abundance		2 mM
17	Adenylation domain YbtE	natural abundance		20-100 nM
18	H2O	natural abundance		90 %
19	D2O	natural abundance		10 %

9 3D 1H-13C NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 bar, Temperature 298 K

#	Name	Isotope labeling	Type	Concentration
20	Loaded-ArCP	[U-99% 13C; U-99% 15N]		0.3-0.4 mM
21	ACES	natural abundance		50 mM
22	TCEP	natural abundance		0.5 mM
23	sodium chloride	natural abundance		150 mM
24	magnesium chloride	natural abundance		1 mM
25	DSS	natural abundance		0.1 mM
26	ATP	natural abundance		2 mM
27	sodium salicylate	[U-100% 13C]		0.5 mM
28	Adenylation domain YbtE	natural abundance		20-100 nM
29	D2O	natural abundance		100 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25787_2n6z.nef
Input source #2: Coordindates	2n6z.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	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:40:ASP:C	1:41:4HJ:N	unknown	unknown	n/a
1:41:4HJ:C	1:42:ILE:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	52	4HJ	O-[(R)-hydroxy{[(3R)-3-hydroxy-4-{[3-({2-[(2-hydroxybenzoyl)sulfanyl]ethyl}amino)-3-oxopropyl]amino}-2,2-dimethyl-4-oxobutyl]oxy}phosphoryl]-L-serine	Assigned chemical shifts, Coordinates

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

-------20--------30--------40--------50--------60--------70--------80--------90---
GTDNRHAADYQQLRERLIQELNLTPQQLHEESNLIQAGLDXIRLMRWLHWFRKNGYRLTLRELYAAPTLAAWNQLMLSRSPE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GTDNRHAADYQQLRERLIQELNLTPQQLHEESNLIQAGLDXIRLMRWLHWFRKNGYRLTLRELYAAPTLAAWNQLMLSRSPE
--------10--------20--------30--------40--------50--------60--------70--------80--

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	82	0	0	100.0

Content subtype: combined_25787_2n6z.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	2		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	903		96.3 (chain: A, length: 82)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	1963 (1)	noe	93.9 (chain: A, length: 82)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	139 (139)	.	90.2 (chain: A, length: 82)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 82, Sequence coverage: 96.3%
- Total number of assignments
  - ¹H chemical shifts: 481
  - ¹³C chemical shifts: 343
  - ¹⁵N chemical shifts: 79
- 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

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 82, Sequence coverage: 93.9%
- Total number of restraints: 1963
- Weight of restraints: 1.0 (1963)
- Potential type of restraints: upper-bound-parabolic (1963)
- Range of distance target values: 2.11, 6.23 (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: 82, Sequence coverage: 90.2%
- Total number of restraints: 139
- Total number of restraints per polymer type: 139
- Weight of restraints: 1.0 (139)
- Potential type of restraints: square-well-parabolic (139)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Carrier Protein, Nonribosomal Peptide Synthetase, Substrate-Loaded, Yersiniabactin