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BMRB: 16100

2KCZ

Solution NMR Structure of the C-Terminal Domain of Protein DR_A0006 from Deinococcus radiodurans, Northeast Structural Genomics Consortium Target DrR147D

Authors

Mills, J.L., Ghosh, A., Garcia, E., Wang, H., Ciccosanti, C., Xiao, R., Nair, R., Everett, J.K., Swapna, G., Acton, T.B., Rost, B., Montelione, G.T., Szyperski, T.

Assembly

DR A0006

Entity

1. DR A0006 (polymer, Thiol state: not present), 155 monomers, 17351.53 Da Detail

MGETVVRDAV TIGKPAEQLY AVWRDLPGLP LLMTHLRSVE VLDDKRSRWT VEAPAPLGAV SWEAELTADE PGKRIAWRSL PGARIENSGE VLFRPAPGAR GTEVVVRLTY RPPGGSAGAV IARMFNQEPS QQLRDDLMRF KREQELGLEH HHHHH

Formula weight

17351.53 Da

Source organism

Deinococcus radiodurans

Exptl. method

solution NMR

Refine. method

simulated annealing, molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 90.3 %, Completeness: 74.6 %, Completeness (bb): 73.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	74.6 % (1329 of 1781)	81.3 % (756 of 930)	65.0 % (453 of 697)	77.9 % (120 of 154)
Backbone	73.2 % (663 of 906)	86.2 % (268 of 311)	61.1 % (276 of 452)	83.2 % (119 of 143)
Sidechain	77.6 % (789 of 1017)	78.8 % (488 of 619)	77.5 % (300 of 387)	9.1 % (1 of 11)
Aromatic	42.6 % (52 of 122)	49.2 % (30 of 61)	38.6 % (22 of 57)	0.0 % (0 of 4)
Methyl	91.5 % (161 of 176)	92.0 % (81 of 88)	90.9 % (80 of 88)

1. DrR147D

MGETVVRDAV TIGKPAEQLY AVWRDLPGLP LLMTHLRSVE VLDDKRSRWT VEAPAPLGAV SWEAELTADE PGKRIAWRSL PGARIENSGE VLFRPAPGAR GTEVVVRLTY RPPGGSAGAV IARMFNQEPS QQLRDDLMRF KREQELGLEH HHHHH

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 4.5

#	Name	Isotope labeling	Concentration
1	DrR147D	[U-99% 13C; U-99% 15N]	0.9 mM
2	D2O	[U-2H]	10 %
3	H2O	natural abundance	90 %
4	DSS	natural abundance	50 uM
5	DTT	natural abundance	10 mM
6	sodium chloride	natural abundance	200 mM
7	sodium azide	natural abundance	0.02 %
8	calcium chloride	natural abundance	5 mM
9	ammonium acetate	natural abundance	20 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 4.5

#	Name	Isotope labeling	Concentration
10	DrR147D	[U-5% 13C; U-99% 15N]	0.9 mM
11	D2O	[U-2H]	10 %
12	H2O	natural abundance	90 %
13	DSS	natural abundance	50 uM
14	DTT	natural abundance	10 mM
15	sodium chloride	natural abundance	200 mM
16	sodium azide	natural abundance	0.02 %
17	calcium chloride	natural abundance	5 mM
18	ammonium acetate	natural abundance	20 mM

LACS Plot; CA

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

Referencing offset: 0.06 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: 0.06 ppm, Outliers: 1 Detail

LACS Plot; HA

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

Referencing offset: -0.11 ppm, Outliers: 5 Detail

Protein Blocks Logo

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

Release date

2009-02-18

Citation

Solution NMR Structure of the C-Terminal Domain of Protein DR_A0006 from Deinococcus radiodurans, Northeast Structural Genomics Consortium Target DrR147D
Mills, J.L., Ghosh, A., Garcia, E., Wang, H., Ciccosanti, C., Xiao, R., Nair, R., Everett, J.K., Swapna, G., Acton, T.B., Rost, B., Montelione, G.T., SZYPERSKI, T.
Not known

Related entities 1. DR A0006, : 1 : 1 : 2 entities Detail

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

#1 Model Varian INOVA (600 MHz)

#2 Model Varian INOVA (750 MHz)

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 4.5

#	Name	Isotope labeling	Concentration
1	DrR147D	[U-99% 13C; U-99% 15N]	0.9 mM
2	D2O	[U-2H]	10 %
3	H2O	natural abundance	90 %
4	DSS	natural abundance	50 uM
5	DTT	natural abundance	10 mM
6	sodium chloride	natural abundance	200 mM
7	sodium azide	natural abundance	0.02 %
8	calcium chloride	natural abundance	5 mM
9	ammonium acetate	natural abundance	20 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 4.5

#	Name	Isotope labeling	Concentration
10	DrR147D	[U-5% 13C; U-99% 15N]	0.9 mM
11	D2O	[U-2H]	10 %
12	H2O	natural abundance	90 %
13	DSS	natural abundance	50 uM
14	DTT	natural abundance	10 mM
15	sodium chloride	natural abundance	200 mM
16	sodium azide	natural abundance	0.02 %
17	calcium chloride	natural abundance	5 mM
18	ammonium acetate	natural abundance	20 mM

2 2D 1H-13C HSQC

Instrument

#1 Model Varian INOVA (600 MHz)

#2 Model Varian INOVA (750 MHz)

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 4.5

#	Name	Isotope labeling	Concentration
1	DrR147D	[U-99% 13C; U-99% 15N]	0.9 mM
2	D2O	[U-2H]	10 %
3	H2O	natural abundance	90 %
4	DSS	natural abundance	50 uM
5	DTT	natural abundance	10 mM
6	sodium chloride	natural abundance	200 mM
7	sodium azide	natural abundance	0.02 %
8	calcium chloride	natural abundance	5 mM
9	ammonium acetate	natural abundance	20 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 4.5

#	Name	Isotope labeling	Concentration
10	DrR147D	[U-5% 13C; U-99% 15N]	0.9 mM
11	D2O	[U-2H]	10 %
12	H2O	natural abundance	90 %
13	DSS	natural abundance	50 uM
14	DTT	natural abundance	10 mM
15	sodium chloride	natural abundance	200 mM
16	sodium azide	natural abundance	0.02 %
17	calcium chloride	natural abundance	5 mM
18	ammonium acetate	natural abundance	20 mM

3 3D HNCO

Instrument

#1 Model Varian INOVA (600 MHz)

#2 Model Varian INOVA (750 MHz)

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 4.5

#	Name	Isotope labeling	Concentration
1	DrR147D	[U-99% 13C; U-99% 15N]	0.9 mM
2	D2O	[U-2H]	10 %
3	H2O	natural abundance	90 %
4	DSS	natural abundance	50 uM
5	DTT	natural abundance	10 mM
6	sodium chloride	natural abundance	200 mM
7	sodium azide	natural abundance	0.02 %
8	calcium chloride	natural abundance	5 mM
9	ammonium acetate	natural abundance	20 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 4.5

#	Name	Isotope labeling	Concentration
10	DrR147D	[U-5% 13C; U-99% 15N]	0.9 mM
11	D2O	[U-2H]	10 %
12	H2O	natural abundance	90 %
13	DSS	natural abundance	50 uM
14	DTT	natural abundance	10 mM
15	sodium chloride	natural abundance	200 mM
16	sodium azide	natural abundance	0.02 %
17	calcium chloride	natural abundance	5 mM
18	ammonium acetate	natural abundance	20 mM

4 3D HNCACB

Instrument

#1 Model Varian INOVA (600 MHz)

#2 Model Varian INOVA (750 MHz)

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 4.5

#	Name	Isotope labeling	Concentration
1	DrR147D	[U-99% 13C; U-99% 15N]	0.9 mM
2	D2O	[U-2H]	10 %
3	H2O	natural abundance	90 %
4	DSS	natural abundance	50 uM
5	DTT	natural abundance	10 mM
6	sodium chloride	natural abundance	200 mM
7	sodium azide	natural abundance	0.02 %
8	calcium chloride	natural abundance	5 mM
9	ammonium acetate	natural abundance	20 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 4.5

#	Name	Isotope labeling	Concentration
10	DrR147D	[U-5% 13C; U-99% 15N]	0.9 mM
11	D2O	[U-2H]	10 %
12	H2O	natural abundance	90 %
13	DSS	natural abundance	50 uM
14	DTT	natural abundance	10 mM
15	sodium chloride	natural abundance	200 mM
16	sodium azide	natural abundance	0.02 %
17	calcium chloride	natural abundance	5 mM
18	ammonium acetate	natural abundance	20 mM

5 3D HNCA

Instrument

#1 Model Varian INOVA (600 MHz)

#2 Model Varian INOVA (750 MHz)

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 4.5

#	Name	Isotope labeling	Concentration
1	DrR147D	[U-99% 13C; U-99% 15N]	0.9 mM
2	D2O	[U-2H]	10 %
3	H2O	natural abundance	90 %
4	DSS	natural abundance	50 uM
5	DTT	natural abundance	10 mM
6	sodium chloride	natural abundance	200 mM
7	sodium azide	natural abundance	0.02 %
8	calcium chloride	natural abundance	5 mM
9	ammonium acetate	natural abundance	20 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 4.5

#	Name	Isotope labeling	Concentration
10	DrR147D	[U-5% 13C; U-99% 15N]	0.9 mM
11	D2O	[U-2H]	10 %
12	H2O	natural abundance	90 %
13	DSS	natural abundance	50 uM
14	DTT	natural abundance	10 mM
15	sodium chloride	natural abundance	200 mM
16	sodium azide	natural abundance	0.02 %
17	calcium chloride	natural abundance	5 mM
18	ammonium acetate	natural abundance	20 mM

6 3D CBCA(CO)NH

Instrument

#1 Model Varian INOVA (600 MHz)

#2 Model Varian INOVA (750 MHz)

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 4.5

#	Name	Isotope labeling	Concentration
1	DrR147D	[U-99% 13C; U-99% 15N]	0.9 mM
2	D2O	[U-2H]	10 %
3	H2O	natural abundance	90 %
4	DSS	natural abundance	50 uM
5	DTT	natural abundance	10 mM
6	sodium chloride	natural abundance	200 mM
7	sodium azide	natural abundance	0.02 %
8	calcium chloride	natural abundance	5 mM
9	ammonium acetate	natural abundance	20 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 4.5

#	Name	Isotope labeling	Concentration
10	DrR147D	[U-5% 13C; U-99% 15N]	0.9 mM
11	D2O	[U-2H]	10 %
12	H2O	natural abundance	90 %
13	DSS	natural abundance	50 uM
14	DTT	natural abundance	10 mM
15	sodium chloride	natural abundance	200 mM
16	sodium azide	natural abundance	0.02 %
17	calcium chloride	natural abundance	5 mM
18	ammonium acetate	natural abundance	20 mM

7 3D HBHA(CO)NH

Instrument

#1 Model Varian INOVA (600 MHz)

#2 Model Varian INOVA (750 MHz)

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 4.5

#	Name	Isotope labeling	Concentration
1	DrR147D	[U-99% 13C; U-99% 15N]	0.9 mM
2	D2O	[U-2H]	10 %
3	H2O	natural abundance	90 %
4	DSS	natural abundance	50 uM
5	DTT	natural abundance	10 mM
6	sodium chloride	natural abundance	200 mM
7	sodium azide	natural abundance	0.02 %
8	calcium chloride	natural abundance	5 mM
9	ammonium acetate	natural abundance	20 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 4.5

#	Name	Isotope labeling	Concentration
10	DrR147D	[U-5% 13C; U-99% 15N]	0.9 mM
11	D2O	[U-2H]	10 %
12	H2O	natural abundance	90 %
13	DSS	natural abundance	50 uM
14	DTT	natural abundance	10 mM
15	sodium chloride	natural abundance	200 mM
16	sodium azide	natural abundance	0.02 %
17	calcium chloride	natural abundance	5 mM
18	ammonium acetate	natural abundance	20 mM

8 3D HCCH-COSY

Instrument

#1 Model Varian INOVA (600 MHz)

#2 Model Varian INOVA (750 MHz)

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 4.5

#	Name	Isotope labeling	Concentration
1	DrR147D	[U-99% 13C; U-99% 15N]	0.9 mM
2	D2O	[U-2H]	10 %
3	H2O	natural abundance	90 %
4	DSS	natural abundance	50 uM
5	DTT	natural abundance	10 mM
6	sodium chloride	natural abundance	200 mM
7	sodium azide	natural abundance	0.02 %
8	calcium chloride	natural abundance	5 mM
9	ammonium acetate	natural abundance	20 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 4.5

#	Name	Isotope labeling	Concentration
10	DrR147D	[U-5% 13C; U-99% 15N]	0.9 mM
11	D2O	[U-2H]	10 %
12	H2O	natural abundance	90 %
13	DSS	natural abundance	50 uM
14	DTT	natural abundance	10 mM
15	sodium chloride	natural abundance	200 mM
16	sodium azide	natural abundance	0.02 %
17	calcium chloride	natural abundance	5 mM
18	ammonium acetate	natural abundance	20 mM

9 3D simultaneous NCaliCaro HH NOESY

Instrument

#1 Model Varian INOVA (600 MHz)

#2 Model Varian INOVA (750 MHz)

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 4.5

#	Name	Isotope labeling	Concentration
1	DrR147D	[U-99% 13C; U-99% 15N]	0.9 mM
2	D2O	[U-2H]	10 %
3	H2O	natural abundance	90 %
4	DSS	natural abundance	50 uM
5	DTT	natural abundance	10 mM
6	sodium chloride	natural abundance	200 mM
7	sodium azide	natural abundance	0.02 %
8	calcium chloride	natural abundance	5 mM
9	ammonium acetate	natural abundance	20 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 4.5

#	Name	Isotope labeling	Concentration
10	DrR147D	[U-5% 13C; U-99% 15N]	0.9 mM
11	D2O	[U-2H]	10 %
12	H2O	natural abundance	90 %
13	DSS	natural abundance	50 uM
14	DTT	natural abundance	10 mM
15	sodium chloride	natural abundance	200 mM
16	sodium azide	natural abundance	0.02 %
17	calcium chloride	natural abundance	5 mM
18	ammonium acetate	natural abundance	20 mM

10 2D 1H-13C HSQC

Instrument

#1 Model Varian INOVA (600 MHz)

#2 Model Varian INOVA (750 MHz)

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 4.5

#	Name	Isotope labeling	Concentration
1	DrR147D	[U-99% 13C; U-99% 15N]	0.9 mM
2	D2O	[U-2H]	10 %
3	H2O	natural abundance	90 %
4	DSS	natural abundance	50 uM
5	DTT	natural abundance	10 mM
6	sodium chloride	natural abundance	200 mM
7	sodium azide	natural abundance	0.02 %
8	calcium chloride	natural abundance	5 mM
9	ammonium acetate	natural abundance	20 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 4.5

#	Name	Isotope labeling	Concentration
10	DrR147D	[U-5% 13C; U-99% 15N]	0.9 mM
11	D2O	[U-2H]	10 %
12	H2O	natural abundance	90 %
13	DSS	natural abundance	50 uM
14	DTT	natural abundance	10 mM
15	sodium chloride	natural abundance	200 mM
16	sodium azide	natural abundance	0.02 %
17	calcium chloride	natural abundance	5 mM
18	ammonium acetate	natural abundance	20 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_16100_2kcz.nef
Input source #2: Coordindates	2kcz.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-------100
MGETVVRDAVTIGKPAEQLYAVWRDLPGLPLLMTHLRSVEVLDDKRSRWTVEAPAPLGAVSWEAELTADEPGKRIAWRSLPGARIENSGEVLFRPAPGAR
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGETVVRDAVTIGKPAEQLYAVWRDLPGLPLLMTHLRSVEVLDDKRSRWTVEAPAPLGAVSWEAELTADEPGKRIAWRSLPGARIENSGEVLFRPAPGAR

-------110-------120-------130-------140-------150-----
GTEVVVRLTYRPPGGSAGAVIARMFNQEPSQQLRDDLMRFKREQELGLEHHHHHH
|||||||||||||||||||||||||||||||||||||||||||||||||||||||
GTEVVVRLTYRPPGGSAGAVIARMFNQEPSQQLRDDLMRFKREQELGLEHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	155	0	0	100.0

Content subtype: combined_16100_2kcz.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1278		87.7 (chain: A, length: 155)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1746 (1)	noe	81.3 (chain: A, length: 155)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	Warning	656 (628)	.	96.1 (chain: A, length: 155)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 155, Sequence coverage: 87.7%
- Total number of assignments
  - ¹H chemical shifts: 729
  - ¹³C chemical shifts: 431
  - ¹⁵N chemical shifts: 118
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	930	729	78.4
¹³C chemical shifts	697	431	61.8
¹⁵N chemical shifts	170	118	69.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	311	264	84.9
¹³C chemical shifts	310	136	43.9
¹⁵N chemical shifts	143	117	81.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	619	465	75.1
¹³C chemical shifts	387	295	76.2
¹⁵N chemical shifts	27	1	3.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	92	79	85.9
¹³C chemical shifts	92	79	85.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	61	30	49.2
¹³C chemical shifts	57	22	38.6
¹⁵N chemical shifts	4	0	0.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 155, Sequence coverage: 81.3%
- Total number of restraints: 1746
- Weight of restraints: 1.0 (1746)
- Potential type of restraints: square-well-parabolic (1746)
- Range of distance target values: 1.38, 5.06 (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: CNS/XPLOR_dihedral_3
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 155, Sequence coverage: 96.1%
- Total number of restraints: 628
- Total number of restraints per polymer type: 628
- Weight of restraints: 1.0 (628)
- Potential type of restraints: square-well-parabolic (628)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords NESGC, Protein structure, PSI

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Found 1 Document (1.042 seconds)

BMRB: 16100

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. DR A0006, : 1 : 1 : 2 entities Detail

Experiments performed 10 experiments Detail

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NMR combined restraints 4 contents Detail