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Found 1 Document (0.537 seconds)

BMRB: 15288

2JQO

NMR solution structure of Bacillus subtilis YobA 21-120: Northeast Structural Genomics Consortium target SR547

Authors

Cort, J.R., Ramelot, T.A., Cort, C.X., Jang, M., Cunningham, K., Ma, L., Xiao, R., Liu, J., Baran, M.C., Acton, T.B., Rost, B., Montelione, G.T., Kennedy, M.A.

Assembly

YobA 21-120

Entity

1. YobA 21-120 (polymer, Thiol state: all free), 108 monomers, 12505.93 Da Detail

MNKNEQNGDE TKMQSLVGYV VLKDNERAIL ITDTKAPGKE DYNLSEGQLM NKFKNNIVIV GLSEIDNTDD LKRGEKIKVW FHTRKESNPP SATIQKYELL LEHHHHHH

Formula weight

12505.93 Da

Source organism

Bacillus subtilis

Exptl. method

solution NMR

Refine. method

torsion angle dynamics, molecular dynamics, simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.3 %, Completeness: 91.4 %, Completeness (bb): 93.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	91.4 % (1187 of 1299)	91.1 % (622 of 683)	90.7 % (450 of 496)	95.8 % (115 of 120)
Backbone	93.6 % (601 of 642)	92.7 % (203 of 219)	93.7 % (298 of 318)	95.2 % (100 of 105)
Sidechain	89.9 % (682 of 759)	90.3 % (419 of 464)	88.6 % (248 of 280)	100.0 % (15 of 15)
Aromatic	48.8 % (41 of 84)	52.4 % (22 of 42)	43.9 % (18 of 41)	100.0 % (1 of 1)
Methyl	96.4 % (106 of 110)	96.4 % (53 of 55)	96.4 % (53 of 55)

1. YobA 21-120

MNKNEQNGDE TKMQSLVGYV VLKDNERAIL ITDTKAPGKE DYNLSEGQLM NKFKNNIVIV GLSEIDNTDD LKRGEKIKVW FHTRKESNPP SATIQKYELL LEHHHHHH

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 4.5

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	0.75 mM
2	dithiothreitol	natural abundance	10 mM
3	calcium chloride	natural abundance	5 mM
4	sodium chloride	natural abundance	100 mM
5	ammonium acetate	natural abundance	20 mM
6	sodium azide	natural abundance	0.02 %
7	H2O	natural abundance	95 %
8	D2O		5 %

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 4.5, Details 13C from 5% 13C-glucose in growth medium

#	Name	Isotope labeling	Concentration
9	entity	[5% 13C; U-100% N15]	0.79 mM
10	dithiothreitol	natural abundance	10 mM
11	calcium chloride	natural abundance	5 mM
12	sodium chloride	natural abundance	100 mM
13	ammonium acetate	natural abundance	20 mM
14	sodium azide	natural abundance	0.02 %
15	H2O	natural abundance	95 %
16	D2O		5 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 4.5

#	Name	Isotope labeling	Concentration
17	entity	[U-100% 13C; U-100% 15N]	0.75 mM
18	dithiothreitol	natural abundance	10 mM
19	calcium chloride	natural abundance	5 mM
20	sodium chloride	natural abundance	100 mM
21	ammonium acetate	natural abundance	20 mM
22	sodium azide	natural abundance	0.02 %
23	D2O		100 %

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: 0.35 ppm, Outliers: 2 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: 0.35 ppm, Outliers: 2 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: -0.1 ppm, Outliers: 1 Detail

LACS Plot; CO

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: 0.56 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2008-02-19

Citation

NMR solution structure of Bacillus subtilis YobA 21-120
Cort, J.R.

Related entities 1. YobA 21-120, : 1 : 2 entities Detail

Experiments performed 12 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 4.5

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	0.75 mM
2	dithiothreitol	natural abundance	10 mM
3	calcium chloride	natural abundance	5 mM
4	sodium chloride	natural abundance	100 mM
5	ammonium acetate	natural abundance	20 mM
6	sodium azide	natural abundance	0.02 %
7	H2O	natural abundance	95 %
8	D2O		5 %

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 4.5, Details 13C from 5% 13C-glucose in growth medium

#	Name	Isotope labeling	Concentration
9	entity	[5% 13C; U-100% N15]	0.79 mM
10	dithiothreitol	natural abundance	10 mM
11	calcium chloride	natural abundance	5 mM
12	sodium chloride	natural abundance	100 mM
13	ammonium acetate	natural abundance	20 mM
14	sodium azide	natural abundance	0.02 %
15	H2O	natural abundance	95 %
16	D2O		5 %

3 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 4.5

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	0.75 mM
2	dithiothreitol	natural abundance	10 mM
3	calcium chloride	natural abundance	5 mM
4	sodium chloride	natural abundance	100 mM
5	ammonium acetate	natural abundance	20 mM
6	sodium azide	natural abundance	0.02 %
7	H2O	natural abundance	95 %
8	D2O		5 %

4 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 4.5

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	0.75 mM
2	dithiothreitol	natural abundance	10 mM
3	calcium chloride	natural abundance	5 mM
4	sodium chloride	natural abundance	100 mM
5	ammonium acetate	natural abundance	20 mM
6	sodium azide	natural abundance	0.02 %
7	H2O	natural abundance	95 %
8	D2O		5 %

5 3D HBHA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 4.5

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	0.75 mM
2	dithiothreitol	natural abundance	10 mM
3	calcium chloride	natural abundance	5 mM
4	sodium chloride	natural abundance	100 mM
5	ammonium acetate	natural abundance	20 mM
6	sodium azide	natural abundance	0.02 %
7	H2O	natural abundance	95 %
8	D2O		5 %

6 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 4.5

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	0.75 mM
2	dithiothreitol	natural abundance	10 mM
3	calcium chloride	natural abundance	5 mM
4	sodium chloride	natural abundance	100 mM
5	ammonium acetate	natural abundance	20 mM
6	sodium azide	natural abundance	0.02 %
7	H2O	natural abundance	95 %
8	D2O		5 %

7 3D HNHA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 4.5

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	0.75 mM
2	dithiothreitol	natural abundance	10 mM
3	calcium chloride	natural abundance	5 mM
4	sodium chloride	natural abundance	100 mM
5	ammonium acetate	natural abundance	20 mM
6	sodium azide	natural abundance	0.02 %
7	H2O	natural abundance	95 %
8	D2O		5 %

8 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 4.5

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	0.75 mM
2	dithiothreitol	natural abundance	10 mM
3	calcium chloride	natural abundance	5 mM
4	sodium chloride	natural abundance	100 mM
5	ammonium acetate	natural abundance	20 mM
6	sodium azide	natural abundance	0.02 %
7	H2O	natural abundance	95 %
8	D2O		5 %

9 3D CCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 4.5

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	0.75 mM
2	dithiothreitol	natural abundance	10 mM
3	calcium chloride	natural abundance	5 mM
4	sodium chloride	natural abundance	100 mM
5	ammonium acetate	natural abundance	20 mM
6	sodium azide	natural abundance	0.02 %
7	H2O	natural abundance	95 %
8	D2O		5 %

10 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 4.5

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	0.75 mM
2	dithiothreitol	natural abundance	10 mM
3	calcium chloride	natural abundance	5 mM
4	sodium chloride	natural abundance	100 mM
5	ammonium acetate	natural abundance	20 mM
6	sodium azide	natural abundance	0.02 %
7	H2O	natural abundance	95 %
8	D2O		5 %

11 3D 1H-13C NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 4.5

#	Name	Isotope labeling	Concentration
1	entity	[U-100% 13C; U-100% 15N]	0.75 mM
2	dithiothreitol	natural abundance	10 mM
3	calcium chloride	natural abundance	5 mM
4	sodium chloride	natural abundance	100 mM
5	ammonium acetate	natural abundance	20 mM
6	sodium azide	natural abundance	0.02 %
7	H2O	natural abundance	95 %
8	D2O		5 %

12 4D 1H-13C-13C-1H HMQC-NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 4.5

#	Name	Isotope labeling	Concentration
17	entity	[U-100% 13C; U-100% 15N]	0.75 mM
18	dithiothreitol	natural abundance	10 mM
19	calcium chloride	natural abundance	5 mM
20	sodium chloride	natural abundance	100 mM
21	ammonium acetate	natural abundance	20 mM
22	sodium azide	natural abundance	0.02 %
23	D2O		100 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15288_2jqo.nef
Input source #2: Coordindates	2jqo.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
MNKNEQNGDETKMQSLVGYVVLKDNERAILITDTKAPGKEDYNLSEGQLMNKFKNNIVIVGLSEIDNTDDLKRGEKIKVWFHTRKESNPPSATIQKYELL
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MNKNEQNGDETKMQSLVGYVVLKDNERAILITDTKAPGKEDYNLSEGQLMNKFKNNIVIVGLSEIDNTDDLKRGEKIKVWFHTRKESNPPSATIQKYELL

--------
LEHHHHHH
||||||||
LEHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	108	0	0	100.0

Content subtype: combined_15288_2jqo.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1208		95.4 (chain: A, length: 108)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1495 (1)	noe	86.1 (chain: A, length: 108)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	58 (1)	hbond	38.9 (chain: A, length: 108)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	78 (78)	.	62.0 (chain: A, length: 108)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 108, Sequence coverage: 95.4%
- Total number of assignments
  - ¹H chemical shifts: 635
  - ¹³C chemical shifts: 456
  - ¹⁵N chemical shifts: 117
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	683	635	93.0
¹³C chemical shifts	496	456	91.9
¹⁵N chemical shifts	123	117	95.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	219	207	94.5
¹³C chemical shifts	216	205	94.9
¹⁵N chemical shifts	105	99	94.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	464	428	92.2
¹³C chemical shifts	280	251	89.6
¹⁵N chemical shifts	18	18	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	58	58	100.0
¹³C chemical shifts	58	58	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	42	18	42.9
¹³C chemical shifts	41	17	41.5
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 108, Sequence coverage: 86.1%
- Total number of restraints: 1495
- Weight of restraints: 1.0 (1495)
- Potential type of restraints: square-well-parabolic (1495)
- Range of distance target values: 2.25, 3.4 (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
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 108, Sequence coverage: 38.9%
  - Total number of restraints: 58
  - Weight of restraints: 1.0 (58)
  - Potential type of restraints: square-well-parabolic (58)
  - Range of distance target values: 2.0, 3.0 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 108, Sequence coverage: 62.0%
- Total number of restraints: 78
- Total number of restraints per polymer type: 78
- Weight of restraints: 1.0 (78)
- Potential type of restraints: square-well-parabolic (78)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords beta barrel, OB-fold, Protein

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Found 1 Document (0.537 seconds)

BMRB: 15288

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. YobA 21-120, : 1 : 2 entities Detail

Experiments performed 12 experiments Detail

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NMR combined restraints 5 contents Detail