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BMRB: 25716

2N5H

PltL-holo

Authors

Jaremko, M.J., Lee, D.JOHN., Burkart, M.D.

Assembly

pyoluteorin type II pep-tidyl carrier protein PltL, holo form

Entity

1. pyoluteorin type II pep-tidyl carrier protein PltL, holo form, entity 1 (polymer, Thiol state: not present), 90 monomers, 10300.70 Da Detail

MDGEEVKEKI RRYIMEDLIG PSAKEDELDD QTPLLEWGIL NSMNIVKLMV YIRDEMGVSI PSTHITGKYF KDLNAISRTV EQLKAESALE

2. 4'-PHOSPHOPANTETHEINE (non-polymer), 358.348 Da

Total weight

10659.048 Da

Max. entity weight

10300.7 Da

Source organism

Pseudomonas protegens Pf-5

Exptl. method

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.9 %, Completeness: 96.2 %, Completeness (bb): 97.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	96.2 % (1024 of 1065)	96.6 % (538 of 557)	95.4 % (396 of 415)	96.8 % (90 of 93)
Backbone	97.0 % (518 of 534)	97.3 % (177 of 182)	97.0 % (257 of 265)	96.6 % (84 of 87)
Sidechain	95.8 % (590 of 616)	96.3 % (361 of 375)	94.9 % (223 of 235)	100.0 % (6 of 6)
Aromatic	80.0 % (40 of 50)	96.0 % (24 of 25)	62.5 % (15 of 24)	100.0 % (1 of 1)
Methyl	100.0 % (108 of 108)	100.0 % (54 of 54)	100.0 % (54 of 54)

1. entity 1

MDGEEVKEKI RRYIMEDLIG PSAKEDELDD QTPLLEWGIL NSMNIVKLMV YIRDEMGVSI PSTHITGKYF KDLNAISRTV EQLKAESALE

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.15 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	potassium phosphate	natural abundance		50 mM
2	TCEP	natural abundance		5 mM
3	sodium azide	natural abundance		0.1 %
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2N5H, Strand ID: A Detail

Release date

2015-09-13

Citation

Structure and Substrate Sequestration in the Pyoluteorin Type II Peptidyl Carrier Protein PltL
Jaremko, M.J., Lee, D.JOHN., Beld, J.J., Opella, S.J., Burkart, M.D.
J. Am. Chem. Soc. (2015), 137, 11546-11549, PubMed 26340431 , DOI 10.1021/jacs.5b04525 , Abstract

Related entities 1. pyoluteorin type II pep-tidyl carrier protein PltL, holo form, entity 1, : 3 entities Detail

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian VS 500 - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.15 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	potassium phosphate	natural abundance		50 mM
2	TCEP	natural abundance		5 mM
3	sodium azide	natural abundance		0.1 %
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

2 2D 1H-13C HSQC

Instrument

Varian VS 500 - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.15 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	potassium phosphate	natural abundance		50 mM
2	TCEP	natural abundance		5 mM
3	sodium azide	natural abundance		0.1 %
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

3 3D CBCA(CO)NH

Instrument

Varian VS 500 - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.15 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	potassium phosphate	natural abundance		50 mM
2	TCEP	natural abundance		5 mM
3	sodium azide	natural abundance		0.1 %
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

4 3D HNCO

Instrument

Varian VS 500 - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.15 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	potassium phosphate	natural abundance		50 mM
2	TCEP	natural abundance		5 mM
3	sodium azide	natural abundance		0.1 %
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

5 3D HNCACB

Instrument

Varian VS 500 - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.15 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	potassium phosphate	natural abundance		50 mM
2	TCEP	natural abundance		5 mM
3	sodium azide	natural abundance		0.1 %
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

6 3D HCCH-TOCSY

Instrument

Varian VS 500 - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.15 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	potassium phosphate	natural abundance		50 mM
2	TCEP	natural abundance		5 mM
3	sodium azide	natural abundance		0.1 %
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

7 3D 1H-15N NOESY

Instrument

Varian VS 500 - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.15 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	potassium phosphate	natural abundance		50 mM
2	TCEP	natural abundance		5 mM
3	sodium azide	natural abundance		0.1 %
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

8 3D 1H-13C NOESY aliphatic

Instrument

Varian VS 500 - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.15 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	potassium phosphate	natural abundance		50 mM
2	TCEP	natural abundance		5 mM
3	sodium azide	natural abundance		0.1 %
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

9 3D 1H-13C NOESY aromatic

Instrument

Varian VS 500 - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.15 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	potassium phosphate	natural abundance		50 mM
2	TCEP	natural abundance		5 mM
3	sodium azide	natural abundance		0.1 %
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

10 3D HCCH-COSY

Instrument

Varian VS 500 - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.15 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	potassium phosphate	natural abundance		50 mM
2	TCEP	natural abundance		5 mM
3	sodium azide	natural abundance		0.1 %
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_25716_2n5h.nef
Input source #2: Coordindates	2n5h.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)
A:42:SER:OG	A:101:PNS:P24	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	91	.	Not matched with CCD	None
A	92	.	Not matched with CCD	None
A	93	.	Not matched with CCD	None
A	94	.	Not matched with CCD	None
A	95	.	Not matched with CCD	None
A	96	.	Not matched with CCD	None
A	97	.	Not matched with CCD	None
A	98	.	Not matched with CCD	None
A	99	.	Not matched with CCD	None
A	100	.	Not matched with CCD	None
A	101	PNS	4'-PHOSPHOPANTETHEINE	Assigned chemical shifts

Sequence alignments

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

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
MDGEEVKEKIRRYIMEDLIGPSAKEDELDDQTPLLEWGILNSMNIVKLMVYIRDEMGVSIPSTHITGKYFKDLNAISRTVEQLKAESALE..........
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||          
MDGEEVKEKIRRYIMEDLIGPSAKEDELDDQTPLLEWGILNSMNIVKLMVYIRDEMGVSIPSTHITGKYFKDLNAISRTVEQLKAESALE          
--------10--------20--------30--------40--------50--------60--------70--------80--------90          

-
X

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	90	11	0	100.0

Content subtype: combined_25716_2n5h.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	1		No information
1	Assigned chemical shifts	nef_chemical_shift_list_assigned_chem_shift_list_1	Warning	1057		89.1 (chain: A, length: 101)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	2453 (1)	noe	98.9 (chain: A, length: 90)

Assigned chemical shifts

Saveframe: nef_chemical_shift_list_assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 101, Sequence coverage: 89.1%
- Total number of assignments
  - ¹H chemical shifts: 563
  - ¹³C chemical shifts: 402
  - ¹⁵N chemical shifts: 92
- 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: 90, Sequence coverage: 98.9%
- Total number of restraints: 2453
- Weight of restraints: 1.0 (2453)
- Potential type of restraints: upper-bound-parabolic (2453)
- Range of distance target values: 2.36, 5.51 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map

Keywords PltL, peptidyl carrier protein, pyoluteorin, pyrrole