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BMRB: 18194

2LT1

1H, 13C, and 15N chemical shift assignments for the 72-residue N-terminal domain of Myxococcus xanthus CarD

Authors

Jimenez, A., Padmanabhan, S., Santoro, J.

Assembly

CarD1-72

Entity

1. CarD1-72 (polymer, Thiol state: not present), 75 monomers, 7879.034 Da Detail

AGHMPEGSAS LQLAVGDRVV YPNQGVCRVS AIDVKEVAGQ KLTFVTMRRE EDGAVVMVPE GKVLAIGVRK VASAE

Formula weight

7879.034 Da

Source organism

Myxococcus xanthus

Exptl. method

solution NMR

Refine. method

simulated annealing, molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 94.2 %, Completeness (bb): 96.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	94.2 % (767 of 814)	95.9 % (402 of 419)	91.5 % (292 of 319)	96.1 % (73 of 76)
Backbone	96.4 % (428 of 444)	96.8 % (150 of 155)	96.3 % (209 of 217)	95.8 % (69 of 72)
Sidechain	92.9 % (406 of 437)	95.5 % (252 of 264)	88.8 % (150 of 169)	100.0 % (4 of 4)
Aromatic	40.9 % (9 of 22)	81.8 % (9 of 11)	0.0 % (0 of 11)
Methyl	96.1 % (98 of 102)	100.0 % (51 of 51)	92.2 % (47 of 51)

1. CarD1-72

AGHMPEGSAS LQLAVGDRVV YPNQGVCRVS AIDVKEVAGQ KLTFVTMRRE EDGAVVMVPE GKVLAIGVRK VASAE

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	CarD1-72	natural abundance	1 mM
2	sodium phosphate	natural abundance	50 mM
3	sodium chloride	natural abundance	100 mM
4	sodium azide	natural abundance	0.01 %
5	beta-mercaptoethanol	natural abundance	2 mM
6	DSS	natural abundance	0.5 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
9	CarD1-72	natural abundance	1 mM
10	sodium phosphate	natural abundance	50 mM
11	sodium chloride	natural abundance	100 mM
12	sodium azide	natural abundance	0.01 %
13	beta-mercaptoethanol	natural abundance	2 mM
14	DSS	natural abundance	0.5 mM
15	D2O	natural abundance	100 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
16	CarD1-72	[U-100% 13C; U-100% 15N]	1 mM
17	sodium phosphate	natural abundance	50 mM
18	sodium chloride	natural abundance	100 mM
19	sodium azide	natural abundance	0.01 %
20	beta-mercaptoethanol	natural abundance	2 mM
21	DSS	natural abundance	0.5 mM
22	H2O	natural abundance	90 %
23	D2O	natural abundance	10 %

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
24	CarD1-72	[U-100% 13C; U-100% 15N]	1 mM
25	sodium phosphate	natural abundance	50 mM
26	sodium chloride	natural abundance	100 mM
27	sodium azide	natural abundance	0.01 %
28	beta-mercaptoethanol	natural abundance	2 mM
29	DSS	natural abundance	0.5 mM
30	D2O	natural abundance	100 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.18 ppm, Outliers: 4 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.18 ppm, Outliers: 4 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.11 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.41 ppm, Outliers: 4 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2LT1, Strand ID: A Detail

Release date

2013-11-10

Citation

Solution NMR structure of the 72-residue N-terminal domain of Myxococcus xanthus CarD
Mirassou, Y., Gallego-Garcia, A., Garcia-Heras, F., Garcia-Moreno, D., Murillo, F.J., Elias-Arnanz, M., Jimenez, A., Padmanabhan, S.
Not known

Related entities 1. CarD1-72, : 1 : 11 entities Detail

Experiments performed 16 experiments Detail

1 2D 1H-1H COSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	CarD1-72	natural abundance	1 mM
2	sodium phosphate	natural abundance	50 mM
3	sodium chloride	natural abundance	100 mM
4	sodium azide	natural abundance	0.01 %
5	beta-mercaptoethanol	natural abundance	2 mM
6	DSS	natural abundance	0.5 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

2 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	CarD1-72	natural abundance	1 mM
2	sodium phosphate	natural abundance	50 mM
3	sodium chloride	natural abundance	100 mM
4	sodium azide	natural abundance	0.01 %
5	beta-mercaptoethanol	natural abundance	2 mM
6	DSS	natural abundance	0.5 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

3 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	CarD1-72	natural abundance	1 mM
2	sodium phosphate	natural abundance	50 mM
3	sodium chloride	natural abundance	100 mM
4	sodium azide	natural abundance	0.01 %
5	beta-mercaptoethanol	natural abundance	2 mM
6	DSS	natural abundance	0.5 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

4 2D 1H-1H COSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
9	CarD1-72	natural abundance	1 mM
10	sodium phosphate	natural abundance	50 mM
11	sodium chloride	natural abundance	100 mM
12	sodium azide	natural abundance	0.01 %
13	beta-mercaptoethanol	natural abundance	2 mM
14	DSS	natural abundance	0.5 mM
15	D2O	natural abundance	100 %

5 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
9	CarD1-72	natural abundance	1 mM
10	sodium phosphate	natural abundance	50 mM
11	sodium chloride	natural abundance	100 mM
12	sodium azide	natural abundance	0.01 %
13	beta-mercaptoethanol	natural abundance	2 mM
14	DSS	natural abundance	0.5 mM
15	D2O	natural abundance	100 %

6 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
9	CarD1-72	natural abundance	1 mM
10	sodium phosphate	natural abundance	50 mM
11	sodium chloride	natural abundance	100 mM
12	sodium azide	natural abundance	0.01 %
13	beta-mercaptoethanol	natural abundance	2 mM
14	DSS	natural abundance	0.5 mM
15	D2O	natural abundance	100 %

7 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
16	CarD1-72	[U-100% 13C; U-100% 15N]	1 mM
17	sodium phosphate	natural abundance	50 mM
18	sodium chloride	natural abundance	100 mM
19	sodium azide	natural abundance	0.01 %
20	beta-mercaptoethanol	natural abundance	2 mM
21	DSS	natural abundance	0.5 mM
22	H2O	natural abundance	90 %
23	D2O	natural abundance	10 %

8 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
16	CarD1-72	[U-100% 13C; U-100% 15N]	1 mM
17	sodium phosphate	natural abundance	50 mM
18	sodium chloride	natural abundance	100 mM
19	sodium azide	natural abundance	0.01 %
20	beta-mercaptoethanol	natural abundance	2 mM
21	DSS	natural abundance	0.5 mM
22	H2O	natural abundance	90 %
23	D2O	natural abundance	10 %

9 3D HNCA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
16	CarD1-72	[U-100% 13C; U-100% 15N]	1 mM
17	sodium phosphate	natural abundance	50 mM
18	sodium chloride	natural abundance	100 mM
19	sodium azide	natural abundance	0.01 %
20	beta-mercaptoethanol	natural abundance	2 mM
21	DSS	natural abundance	0.5 mM
22	H2O	natural abundance	90 %
23	D2O	natural abundance	10 %

10 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
16	CarD1-72	[U-100% 13C; U-100% 15N]	1 mM
17	sodium phosphate	natural abundance	50 mM
18	sodium chloride	natural abundance	100 mM
19	sodium azide	natural abundance	0.01 %
20	beta-mercaptoethanol	natural abundance	2 mM
21	DSS	natural abundance	0.5 mM
22	H2O	natural abundance	90 %
23	D2O	natural abundance	10 %

11 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
16	CarD1-72	[U-100% 13C; U-100% 15N]	1 mM
17	sodium phosphate	natural abundance	50 mM
18	sodium chloride	natural abundance	100 mM
19	sodium azide	natural abundance	0.01 %
20	beta-mercaptoethanol	natural abundance	2 mM
21	DSS	natural abundance	0.5 mM
22	H2O	natural abundance	90 %
23	D2O	natural abundance	10 %

12 3D HBHA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
16	CarD1-72	[U-100% 13C; U-100% 15N]	1 mM
17	sodium phosphate	natural abundance	50 mM
18	sodium chloride	natural abundance	100 mM
19	sodium azide	natural abundance	0.01 %
20	beta-mercaptoethanol	natural abundance	2 mM
21	DSS	natural abundance	0.5 mM
22	H2O	natural abundance	90 %
23	D2O	natural abundance	10 %

13 3D HBHANH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
16	CarD1-72	[U-100% 13C; U-100% 15N]	1 mM
17	sodium phosphate	natural abundance	50 mM
18	sodium chloride	natural abundance	100 mM
19	sodium azide	natural abundance	0.01 %
20	beta-mercaptoethanol	natural abundance	2 mM
21	DSS	natural abundance	0.5 mM
22	H2O	natural abundance	90 %
23	D2O	natural abundance	10 %

14 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
24	CarD1-72	[U-100% 13C; U-100% 15N]	1 mM
25	sodium phosphate	natural abundance	50 mM
26	sodium chloride	natural abundance	100 mM
27	sodium azide	natural abundance	0.01 %
28	beta-mercaptoethanol	natural abundance	2 mM
29	DSS	natural abundance	0.5 mM
30	D2O	natural abundance	100 %

15 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
24	CarD1-72	[U-100% 13C; U-100% 15N]	1 mM
25	sodium phosphate	natural abundance	50 mM
26	sodium chloride	natural abundance	100 mM
27	sodium azide	natural abundance	0.01 %
28	beta-mercaptoethanol	natural abundance	2 mM
29	DSS	natural abundance	0.5 mM
30	D2O	natural abundance	100 %

16 3D 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
24	CarD1-72	[U-100% 13C; U-100% 15N]	1 mM
25	sodium phosphate	natural abundance	50 mM
26	sodium chloride	natural abundance	100 mM
27	sodium azide	natural abundance	0.01 %
28	beta-mercaptoethanol	natural abundance	2 mM
29	DSS	natural abundance	0.5 mM
30	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_18194_2lt1.nef
Input source #2: Coordindates	2lt1.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-----
AGHMPEGSASLQLAVGDRVVYPNQGVCRVSAIDVKEVAGQKLTFVTMRREEDGAVVMVPEGKVLAIGVRKVASAE
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
AGHMPEGSASLQLAVGDRVVYPNQGVCRVSAIDVKEVAGQKLTFVTMRREEDGAVVMVPEGKVLAIGVRKVASAE

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	75	0	0	100.0

Content subtype: combined_18194_2lt1.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	773		98.7 (chain: A, length: 75)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	1035 (1)	noe	94.7 (chain: A, length: 75)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	121 (121)	.	97.3 (chain: A, length: 75)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 75, Sequence coverage: 98.7%
- Total number of assignments
  - ¹H chemical shifts: 404
  - ¹³C chemical shifts: 296
  - ¹⁵N chemical shifts: 73
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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)
12	GLN	CD	180.796
23	ASN	CG	178.197
24	GLN	CD	178.293
40	GLN	CD	180.562
49	ARG	CZ	159.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	419	404	96.4
¹³C chemical shifts	319	291	91.2
¹⁵N chemical shifts	81	73	90.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	155	149	96.1
¹³C chemical shifts	150	141	94.0
¹⁵N chemical shifts	72	68	94.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	264	255	96.6
¹³C chemical shifts	169	150	88.8
¹⁵N chemical shifts	9	5	55.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	54	51	94.4
¹³C chemical shifts	54	47	87.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	11	9	81.8
¹³C chemical shifts	11	0	0.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 75, Sequence coverage: 94.7%
- Total number of restraints: 1035
- Weight of restraints: 1.0 (1035)
- Potential type of restraints: upper-bound-parabolic (1035)
- Range of distance target values: 2.44, 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: 75, Sequence coverage: 97.3%
- Total number of restraints: 121
- Total number of restraints per polymer type: 121
- Weight of restraints: 1.0 (121)
- Potential type of restraints: square-well-parabolic (121)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords CarD, CarD_TRCF, CarG, CdnL, Myxococcus xanthus, PF02559, RNA polymerase interacting domain

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Found 1 Document (0.68 seconds)

BMRB: 18194

Sample #1

Sample #2

Sample #3

Sample #4

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. CarD1-72, : 1 : 11 entities Detail

Experiments performed 16 experiments Detail

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NMR combined restraints 4 contents Detail