BMRBj - BMREntryMaster

Found 1 Document (0.683 seconds)

BMRB: 17886

2M5R

Backbone chemical shift assignments of holo-acyl carrier protein of Leishmania major

Authors

Kumar, A., Surolia, A., Sundd, M.

Assembly

holo-acyl carrier protein monomer

Entity

1. acyl carrier protein polypetide (polymer, Thiol state: all free), 80 monomers, 8996.134 Da Detail

MNDVLTRVLE VVKNFEKVDA SKVTPESHFV KDLGLNSLDV VEVVFAIEQE FILDIPDHDA EKIQSIPDAV EYIAQNPMAK

2. PNS (non-polymer), 358.348 Da

Total weight

9354.481 Da

Max. entity weight

8996.134 Da

Source organism

Leishmania major strain Friedlin

Exptl. method

solution NMR

Refine. method

DGSA-distance geometry simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 89.7 %, Completeness (bb): 98.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.7 % (842 of 939)	86.8 % (420 of 484)	91.1 % (339 of 372)	100.0 % (83 of 83)
Backbone	98.7 % (466 of 472)	99.4 % (156 of 157)	97.9 % (234 of 239)	100.0 % (76 of 76)
Sidechain	83.3 % (455 of 546)	80.7 % (264 of 327)	86.8 % (184 of 212)	100.0 % (7 of 7)
Aromatic	44.6 % (25 of 56)	42.9 % (12 of 28)	46.4 % (13 of 28)
Methyl	91.1 % (102 of 112)	96.4 % (54 of 56)	85.7 % (48 of 56)

1. acyl carrier protein polypetide

MNDVLTRVLE VVKNFEKVDA SKVTPESHFV KDLGLNSLDV VEVVFAIEQE FILDIPDHDA EKIQSIPDAV EYIAQNPMAK

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.0 (±0.1), Details In sample protease inhibitor coocktail (from Sigma)was used to avoid protease degradation

#	Name	Isotope labeling	Concentration
1	acyl_carrier_protein_polypetide	natural abundance	2 mM
2	4'-PHOSPHOPANTETHEINE	natural abundance	2 mM
3	sodium phosphate	[U-99% 13C; U-99% 15N]	1.0 ~ 2.0 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	indirect	0.0
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.0

Referencing offset: 0.21 ppm, Outliers: 3 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	indirect	0.0
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.0

Referencing offset: 0.21 ppm, Outliers: 3 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	indirect	0.0
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.0

Referencing offset: 0.13 ppm, Outliers: 2 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	indirect	0.0
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.0

Referencing offset: 2.65 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2M5R, Strand ID: A Detail

Release date

2012-01-31

Citation

Backbone and side chain 1H, 15N & 13C chemical shift assignments of the holo-acyl carrier protein (ACP) of Leishmania major
Kumar, A., Surolia, A., Sundd, M.
Biomol. NMR Assign. (2012), 6, 221-223, PubMed 22278299 , DOI 10.1007/s12104-012-9362-5 , Abstract

Related entities 1. acyl carrier protein polypetide, : 1 : 1 : 1 : 1 : 224 entities Detail

Experiments performed 7 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.0 (±0.1), Details In sample protease inhibitor coocktail (from Sigma)was used to avoid protease degradation

#	Name	Isotope labeling	Concentration
1	acyl_carrier_protein_polypetide	natural abundance	2 mM
2	4'-PHOSPHOPANTETHEINE	natural abundance	2 mM
3	sodium phosphate	[U-99% 13C; U-99% 15N]	1.0 ~ 2.0 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

2 3D HNCACB

Instrument

Bruker Avance - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	acyl_carrier_protein_polypetide	natural abundance	2 mM
2	4'-PHOSPHOPANTETHEINE	natural abundance	2 mM
3	sodium phosphate	[U-99% 13C; U-99% 15N]	1.0 ~ 2.0 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

3 3D CBCA(CO)NH

Instrument

Bruker Avance - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	acyl_carrier_protein_polypetide	natural abundance	2 mM
2	4'-PHOSPHOPANTETHEINE	natural abundance	2 mM
3	sodium phosphate	[U-99% 13C; U-99% 15N]	1.0 ~ 2.0 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

4 3D HNCA

Instrument

Bruker Avance - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	acyl_carrier_protein_polypetide	natural abundance	2 mM
2	4'-PHOSPHOPANTETHEINE	natural abundance	2 mM
3	sodium phosphate	[U-99% 13C; U-99% 15N]	1.0 ~ 2.0 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

5 3D HNCO

Instrument

Bruker Avance - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	acyl_carrier_protein_polypetide	natural abundance	2 mM
2	4'-PHOSPHOPANTETHEINE	natural abundance	2 mM
3	sodium phosphate	[U-99% 13C; U-99% 15N]	1.0 ~ 2.0 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

6 3D C(CO)NH

Instrument

Bruker Avance - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	acyl_carrier_protein_polypetide	natural abundance	2 mM
2	4'-PHOSPHOPANTETHEINE	natural abundance	2 mM
3	sodium phosphate	[U-99% 13C; U-99% 15N]	1.0 ~ 2.0 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

7 3D 1H-15N TOCSY

Instrument

Bruker Avance - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	acyl_carrier_protein_polypetide	natural abundance	2 mM
2	4'-PHOSPHOPANTETHEINE	natural abundance	2 mM
3	sodium phosphate	[U-99% 13C; U-99% 15N]	1.0 ~ 2.0 mM
4	H2O	natural abundance	90 %
5	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_17886_2m5r.nef
Input source #2: Coordindates	2m5r.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)
1:37:SER:OG	2:1:PNS:P24	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	PNS	4'-PHOSPHOPANTETHEINE	None

Sequence alignments

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

--------10--------20--------30--------40--------50--------60--------70--------80
MNDVLTRVLEVVKNFEKVDASKVTPESHFVKDLGLNSLDVVEVVFAIEQEFILDIPDHDAEKIQSIPDAVEYIAQNPMAK
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MNDVLTRVLEVVKNFEKVDASKVTPESHFVKDLGLNSLDVVEVVFAIEQEFILDIPDHDAEKIQSIPDAVEYIAQNPMAK

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	80	0	0	100.0

Content subtype: combined_17886_2m5r.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	1		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	829		100.0 (chain: A, length: 80)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	2217 (1)	noe	100.0 (chain: A, length: 80)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	113 (113)	.	95.0 (chain: A, length: 80)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 80, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 413
  - ¹³C chemical shifts: 333
  - ¹⁵N chemical shifts: 83
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
28	HIS	HD1	7.118

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	484	411	84.9
¹³C chemical shifts	372	333	89.5
¹⁵N chemical shifts	84	83	98.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	157	155	98.7
¹³C chemical shifts	160	154	96.3
¹⁵N chemical shifts	76	76	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	327	256	78.3
¹³C chemical shifts	212	179	84.4
¹⁵N chemical shifts	8	7	87.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	58	53	91.4
¹³C chemical shifts	58	48	82.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	28	12	42.9
¹³C chemical shifts	28	13	46.4

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 80, Sequence coverage: 100.0%
- Total number of restraints: 2211
- Weight of restraints: 1.0 (2211)
- Potential type of restraints: square-well-parabolic (2211)
- Range of distance target values: 2.0, 5.4 (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

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 80, Sequence coverage: 95.0%
- Total number of restraints: 113
- Total number of restraints per polymer type: 113
- Weight of restraints: 1.0 (113)
- Potential type of restraints: square-well-parabolic (113)
- Dihedral angle restraints per residue
  - Chain_ID: A

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Found 1 Document (0.683 seconds)

BMRB: 17886

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. acyl carrier protein polypetide, : 1 : 1 : 1 : 1 : 224 entities Detail

Experiments performed 7 experiments Detail

Instrument

Sample

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Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

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Sample

NMR combined restraints 4 contents Detail