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BMRB: 19479

2MD9

Solution Structure of an Active Site Mutant Pepitdyl Carrier Protein

Authors

Tufar, P., Rahighi, S., Kraas, F.I., Kirchner, D.K., Loehr, F., Henrich, E., Koepke, J., Dikic, I., Guentert, P., Marahiel, M.A., Doetsch, V.

Assembly

Active Site Mutant Pepitdyl Carrier Protein

Entity

1. Active Site Mutant Pepitdyl Carrier Protein (polymer, Thiol state: not present), 90 monomers, 9957.299 Da Detail

PVTEAQYVAP TNAVESKLAE IWERVLGVSG IGILDNFFQI GGHALKAMAV AAQVHREYQV ELPLKVLFAQ PTIKALAQYV ATRSHHHHHH

Formula weight

9957.299 Da

Source organism

Brevibacillus brevis

Exptl. method

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 95.6 %, Completeness: 82.2 %, Completeness (bb): 78.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	82.2 % (859 of 1045)	89.9 % (480 of 534)	71.6 % (298 of 416)	85.3 % (81 of 95)
Backbone	78.9 % (420 of 532)	92.8 % (168 of 181)	65.3 % (173 of 265)	91.9 % (79 of 86)
Sidechain	87.0 % (520 of 598)	88.4 % (312 of 353)	87.3 % (206 of 236)	22.2 % (2 of 9)
Aromatic	63.3 % (62 of 98)	75.5 % (37 of 49)	50.0 % (24 of 48)	100.0 % (1 of 1)
Methyl	98.4 % (124 of 126)	100.0 % (63 of 63)	96.8 % (61 of 63)

1. PCP

PVTEAQYVAP TNAVESKLAE IWERVLGVSG IGILDNFFQI GGHALKAMAV AAQVHREYQV ELPLKVLFAQ PTIKALAQYV ATRSHHHHHH

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	PCP	[U-100% 13C; U-100% 15N]		0.7 mM
2	sodium phosphate	natural abundance		50 mM
3	DSS	natural abundance		0.15 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

LACS Plot; CA

Referencing offset: -0.59 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.59 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.03 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2MD9, Strand ID: A Detail

Release date

2014-04-21

Citation

Crystal structure of a PCP/Sfp complex reveals the structural basis for carrier protein posttranslational modification
Tufar, P., Rahighi, S., Kraas, F.I., Kirchner, D.K., Lohr, F., Henrich, E., Kopke, J., Dikic, I., Guntert, P., Marahiel, M.A., Dotsch, V.
Chem. Biol. (2014), 21, 552-562, PubMed 24704508 , DOI 10.1016/j.chembiol.2014.02.014 , Abstract

Related entities 1. Active Site Mutant Pepitdyl Carrier Protein, : 1 : 1 : 1 : 171 entities Detail

Interaction partners 1. Active Site Mutant Pepitdyl Carrier Protein, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 8 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	PCP	[U-100% 13C; U-100% 15N]		0.7 mM
2	sodium phosphate	natural abundance		50 mM
3	DSS	natural abundance		0.15 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

2 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	PCP	[U-100% 13C; U-100% 15N]		0.7 mM
2	sodium phosphate	natural abundance		50 mM
3	DSS	natural abundance		0.15 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

3 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	PCP	[U-100% 13C; U-100% 15N]		0.7 mM
2	sodium phosphate	natural abundance		50 mM
3	DSS	natural abundance		0.15 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

4 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	PCP	[U-100% 13C; U-100% 15N]		0.7 mM
2	sodium phosphate	natural abundance		50 mM
3	DSS	natural abundance		0.15 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

5 3D H(CCCO)NH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	PCP	[U-100% 13C; U-100% 15N]		0.7 mM
2	sodium phosphate	natural abundance		50 mM
3	DSS	natural abundance		0.15 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

6 3D (H)C(CCO)NH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	PCP	[U-100% 13C; U-100% 15N]		0.7 mM
2	sodium phosphate	natural abundance		50 mM
3	DSS	natural abundance		0.15 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

7 3D 1H-15N NOESY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	PCP	[U-100% 13C; U-100% 15N]		0.7 mM
2	sodium phosphate	natural abundance		50 mM
3	DSS	natural abundance		0.15 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

8 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	PCP	[U-100% 13C; U-100% 15N]		0.7 mM
2	sodium phosphate	natural abundance		50 mM
3	DSS	natural abundance		0.15 mM
4	H2O	natural abundance		95 %
5	D2O	natural abundance		5 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19479_2md9.nef
Input source #2: Coordindates	2md9.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--------90-
PVTEAQYVAPTNAVESKLAEIWERVLGVSGIGILDNFFQIGGHALKAMAVAAQVHREYQVELPLKVLFAQPTIKALAQYVATRSHHHHHH
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PVTEAQYVAPTNAVESKLAEIWERVLGVSGIGILDNFFQIGGHALKAMAVAAQVHREYQVELPLKVLFAQPTIKALAQYVATRSHHHHHH
--------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	90	0	0	100.0

Content subtype: combined_19479_2md9.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	853		95.6 (chain: A, length: 90)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	1743 (1)	noe	94.4 (chain: A, length: 90)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	140 (140)	.	91.1 (chain: A, length: 90)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 90, Sequence coverage: 95.6%
- Total number of assignments
  - ¹H chemical shifts: 482
  - ¹³C chemical shifts: 292
  - 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

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: 94.4%
- Total number of restraints: 1743
- Weight of restraints: 1.0 (1743)
- Potential type of restraints: upper-bound-parabolic (1743)
- Range of distance target values: 2.4, 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: 90, Sequence coverage: 91.1%
- 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 Carrier Protein, Protein