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Found 1 Document (0.774 seconds)

BMRB: 15203

2JOV

NMR Structure of Clostridium Perfringens Protein CPE0013. Northeast Structural Genomics Target CpR31.

Authors

Ding, K., Ramelot, T.A., Anklin, C., Wang, H., Nwosu, C., Cunningham, K., Ma, L., Xiao, R., Liu, J., Baran, M.C., Swapna, G.V.T., Acton, T.B., Rost, B., Montelione, G.T., Kennedy, M.A.

Assembly

CPE0013 monomer

Entity

1. CPE0013 monomer (polymer, Thiol state: all free), 85 monomers, 9659.120 Da Detail

MHKDIFTSVV RVRGSKKYNV VPVKSNKPVE ISKWIDFSNV LSRLYVGVPT KSGNVVCKNI MNTGVDIICT KNLPKDSLEH HHHHH

Formula weight

9659.12 Da

Source organism

Clostridium perfringens

Exptl. method

solution NMR

Refine. method

DGSA-distance geometry simulated annealing

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 91.8 %, Completeness: 88.1 %, Completeness (bb): 89.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	88.1 % (894 of 1015)	88.4 % (467 of 528)	87.2 % (347 of 398)	89.9 % (80 of 89)
Backbone	89.6 % (450 of 502)	90.6 % (154 of 170)	88.8 % (223 of 251)	90.1 % (73 of 81)
Sidechain	87.2 % (518 of 594)	87.4 % (313 of 358)	86.8 % (198 of 228)	87.5 % (7 of 8)
Aromatic	44.7 % (34 of 76)	44.7 % (17 of 38)	45.9 % (17 of 37)	0.0 % (0 of 1)
Methyl	100.0 % (100 of 100)	100.0 % (50 of 50)	100.0 % (50 of 50)

1. CPE0013

MHKDIFTSVV RVRGSKKYNV VPVKSNKPVE ISKWIDFSNV LSRLYVGVPT KSGNVVCKNI MNTGVDIICT KNLPKDSLEH HHHHH

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 (±1) atm, Temperature 293 (±1) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Concentration
1	protein	[U-100% 13C; U-100% 15N]	1 mM
2	MES	natural abundance	20 mM
3	NaCl	natural abundance	100 mM
4	DTT	natural abundance	10 mM
5	CaCl2	natural abundance	5 mM
6	NaN3	natural abundance	0.02 %
7	D2O	natural abundance	5 %

Sample #2

Solvent system 100% D2O, Pressure 1 (±1) atm, Temperature 293 (±1) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Concentration
8	protein	[U-100% 13C; U-100% 15N]	1 mM
9	MES	natural abundance	20 mM
10	NaCl	natural abundance	100 mM
11	DTT	natural abundance	10 mM
12	CaCl2	natural abundance	5 mM
13	NaN3	natural abundance	0.02 %

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 (±1) atm, Temperature 293 (±1) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Concentration
14	protein	[U-5% 13C; U-100% 15N]	1 mM
15	MES	natural abundance	20 mM
16	NaCl	natural abundance	100 mM
17	DTT	natural abundance	10 mM
18	CaCl2	natural abundance	5 mM
19	NaN3	natural abundance	0.02 %
20	D2O	natural abundance	5 %

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: 0.01 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: 0.03 ppm, Outliers: 4 Detail

Protein Blocks Logo

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

Release date

2007-05-03

Citation

NMR structure of Clostridium perfringens protein CPE0013
Ding, K., Ramelot, T.A., Wang, H., Nwosu, C., Montelione, G.T., Kennedy, M.A.

Related entities 1. CPE0013 monomer, : 1 : 1 entities Detail

Experiments performed 13 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 (±1) atm, Temperature 293 (±1) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Concentration
1	protein	[U-100% 13C; U-100% 15N]	1 mM
2	MES	natural abundance	20 mM
3	NaCl	natural abundance	100 mM
4	DTT	natural abundance	10 mM
5	CaCl2	natural abundance	5 mM
6	NaN3	natural abundance	0.02 %
7	D2O	natural abundance	5 %

2 3D HNCO

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 (±1) atm, Temperature 293 (±1) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Concentration
1	protein	[U-100% 13C; U-100% 15N]	1 mM
2	MES	natural abundance	20 mM
3	NaCl	natural abundance	100 mM
4	DTT	natural abundance	10 mM
5	CaCl2	natural abundance	5 mM
6	NaN3	natural abundance	0.02 %
7	D2O	natural abundance	5 %

3 3D HNCA

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 (±1) atm, Temperature 293 (±1) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Concentration
1	protein	[U-100% 13C; U-100% 15N]	1 mM
2	MES	natural abundance	20 mM
3	NaCl	natural abundance	100 mM
4	DTT	natural abundance	10 mM
5	CaCl2	natural abundance	5 mM
6	NaN3	natural abundance	0.02 %
7	D2O	natural abundance	5 %

4 3D HN(CO)CA

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 (±1) atm, Temperature 293 (±1) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Concentration
1	protein	[U-100% 13C; U-100% 15N]	1 mM
2	MES	natural abundance	20 mM
3	NaCl	natural abundance	100 mM
4	DTT	natural abundance	10 mM
5	CaCl2	natural abundance	5 mM
6	NaN3	natural abundance	0.02 %
7	D2O	natural abundance	5 %

5 3D CBCA(CO)NH

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 (±1) atm, Temperature 293 (±1) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Concentration
1	protein	[U-100% 13C; U-100% 15N]	1 mM
2	MES	natural abundance	20 mM
3	NaCl	natural abundance	100 mM
4	DTT	natural abundance	10 mM
5	CaCl2	natural abundance	5 mM
6	NaN3	natural abundance	0.02 %
7	D2O	natural abundance	5 %

6 3D HNCACB

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 (±1) atm, Temperature 293 (±1) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Concentration
1	protein	[U-100% 13C; U-100% 15N]	1 mM
2	MES	natural abundance	20 mM
3	NaCl	natural abundance	100 mM
4	DTT	natural abundance	10 mM
5	CaCl2	natural abundance	5 mM
6	NaN3	natural abundance	0.02 %
7	D2O	natural abundance	5 %

7 2D 1H-13C HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 (±1) atm, Temperature 293 (±1) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Concentration
8	protein	[U-100% 13C; U-100% 15N]	1 mM
9	MES	natural abundance	20 mM
10	NaCl	natural abundance	100 mM
11	DTT	natural abundance	10 mM
12	CaCl2	natural abundance	5 mM
13	NaN3	natural abundance	0.02 %

8 2D 1H-13C HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 (±1) atm, Temperature 293 (±1) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Concentration
14	protein	[U-5% 13C; U-100% 15N]	1 mM
15	MES	natural abundance	20 mM
16	NaCl	natural abundance	100 mM
17	DTT	natural abundance	10 mM
18	CaCl2	natural abundance	5 mM
19	NaN3	natural abundance	0.02 %
20	D2O	natural abundance	5 %

9 3D HBHA(CO)NH

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 (±1) atm, Temperature 293 (±1) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Concentration
1	protein	[U-100% 13C; U-100% 15N]	1 mM
2	MES	natural abundance	20 mM
3	NaCl	natural abundance	100 mM
4	DTT	natural abundance	10 mM
5	CaCl2	natural abundance	5 mM
6	NaN3	natural abundance	0.02 %
7	D2O	natural abundance	5 %

10 3D HCCH-TOCSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 (±1) atm, Temperature 293 (±1) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Concentration
8	protein	[U-100% 13C; U-100% 15N]	1 mM
9	MES	natural abundance	20 mM
10	NaCl	natural abundance	100 mM
11	DTT	natural abundance	10 mM
12	CaCl2	natural abundance	5 mM
13	NaN3	natural abundance	0.02 %

11 3D 1H-15N NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 (±1) atm, Temperature 293 (±1) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Concentration
1	protein	[U-100% 13C; U-100% 15N]	1 mM
2	MES	natural abundance	20 mM
3	NaCl	natural abundance	100 mM
4	DTT	natural abundance	10 mM
5	CaCl2	natural abundance	5 mM
6	NaN3	natural abundance	0.02 %
7	D2O	natural abundance	5 %

12 3D 1H-13C NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 (±1) atm, Temperature 293 (±1) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Concentration
1	protein	[U-100% 13C; U-100% 15N]	1 mM
2	MES	natural abundance	20 mM
3	NaCl	natural abundance	100 mM
4	DTT	natural abundance	10 mM
5	CaCl2	natural abundance	5 mM
6	NaN3	natural abundance	0.02 %
7	D2O	natural abundance	5 %

13 3D 1H-13C NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 (±1) atm, Temperature 293 (±1) K, pH 6.5 (±0.2)

#	Name	Isotope labeling	Concentration
8	protein	[U-100% 13C; U-100% 15N]	1 mM
9	MES	natural abundance	20 mM
10	NaCl	natural abundance	100 mM
11	DTT	natural abundance	10 mM
12	CaCl2	natural abundance	5 mM
13	NaN3	natural abundance	0.02 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15203_2jov.nef
Input source #2: Coordindates	2jov.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-----
MHKDIFTSVVRVRGSKKYNVVPVKSNKPVEISKWIDFSNVLSRLYVGVPTKSGNVVCKNIMNTGVDIICTKNLPKDSLEHHHHHH
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MHKDIFTSVVRVRGSKKYNVVPVKSNKPVEISKWIDFSNVLSRLYVGVPTKSGNVVCKNIMNTGVDIICTKNLPKDSLEHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	85	0	0	100.0

Content subtype: combined_15203_2jov.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	894		91.8 (chain: A, length: 85)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1078 (1)	noe	90.6 (chain: A, length: 85)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	28 (1)	hbond	24.7 (chain: A, length: 85)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	62 (62)	.	58.8 (chain: A, length: 85)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 85, Sequence coverage: 91.8%
- Total number of assignments
  - ¹H chemical shifts: 467
  - ¹³C chemical shifts: 347
  - ¹⁵N chemical shifts: 80
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	528	467	88.4
¹³C chemical shifts	398	347	87.2
¹⁵N chemical shifts	92	80	87.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	170	154	90.6
¹³C chemical shifts	170	149	87.6
¹⁵N chemical shifts	81	73	90.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	358	313	87.4
¹³C chemical shifts	228	198	86.8
¹⁵N chemical shifts	11	7	63.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	52	51	98.1
¹³C chemical shifts	52	51	98.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	38	17	44.7
¹³C chemical shifts	37	17	45.9
¹⁵N chemical shifts	1	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: 85, Sequence coverage: 90.6%
- Total number of restraints: 1074
- Weight of restraints: 1.0 (1074)
- Potential type of restraints: square-well-parabolic (1074)
- Range of distance target values: 2.35, 3.4 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_4
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 85, Sequence coverage: 24.7%
  - Total number of restraints: 28
  - Weight of restraints: 1.0 (28)
  - Potential type of restraints: square-well-parabolic (28)
  - Range of distance target values: 2.05, 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_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 85, Sequence coverage: 58.8%
- Total number of restraints: 62
- Total number of restraints per polymer type: 62
- Weight of restraints: 1.0 (62)
- Potential type of restraints: square-well-parabolic (62)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords alpha + beta sandwich

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Found 1 Document (0.774 seconds)

BMRB: 15203

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. CPE0013 monomer, : 1 : 1 entities Detail

Experiments performed 13 experiments Detail

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NMR combined restraints 5 contents Detail