BMRBj - BMREntryMaster

Found 1 Document (0.787 seconds)

BMRB: 15793

2K4B

CopR Repressor Structure

Authors

Cantini, F., Banci, L., Magnani, D., Solioz, M.

Assembly

CopR-NTD

Entity

1. CopR-NTD (polymer, Thiol state: not present), 99 monomers, 11753.28 Da Detail

MSYYHHHHHH DYDIPTTENL YFQGAMNEVE FNVSNAELIV MRVIWSLGEA RVDEIYAQIP QELEWSLATV KTLLGRLVKK EMLSTEKEGR KFVYRPLME

Formula weight

11753.28 Da

Source organism

Lactococcus lactis

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts, heteronucl_NOEs, heteronucl_T1_relaxation, heteronucl_T2_relaxation

Chem. Shift Complete

Sequence coverage: 66.7 %, Completeness: 55.5 %, Completeness (bb): 60.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	55.5 % (670 of 1207)	56.5 % (354 of 626)	52.9 % (252 of 476)	61.0 % (64 of 105)
Backbone	60.4 % (355 of 588)	62.3 % (124 of 199)	58.7 % (172 of 293)	61.5 % (59 of 96)
Sidechain	52.1 % (372 of 714)	53.9 % (230 of 427)	49.3 % (137 of 278)	55.6 % (5 of 9)
Aromatic	16.7 % (21 of 126)	30.2 % (19 of 63)	0.0 % (0 of 61)	100.0 % (2 of 2)
Methyl	75.0 % (84 of 112)	75.0 % (42 of 56)	75.0 % (42 of 56)

1. CopR-NTD

MSYYHHHHHH DYDIPTTENL YFQGAMNEVE FNVSNAELIV MRVIWSLGEA RVDEIYAQIP QELEWSLATV KTLLGRLVKK EMLSTEKEGR KFVYRPLME

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	CopR-NTD	[U-99% 13C; U-99% 15N]		0.2 (±0.05) mM
2	NaPi			50 mM
3	NaCl			100 mM
4	H2O	natural abundance		90 %
5	D2O			10 %

LACS Plot; CA

Referencing offset: -0.16 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: -0.16 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: 0.12 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: -0.29 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2K4B, Strand ID: A Detail

Heteronucl. T₁

49 T₁ values in 1 lists
Coherence Sz, Field strength (¹H) 700.13 MHz, Pressure 1 atm, Temperature 298 K, pH 7.5 Detail

Heteronucl. T₂

49 T₂ values in 1 lists
Coherence S(+,-), Field strength (¹H) 700.13 MHz, Pressure 1 atm, Temperature 298 K, pH 7.5 Detail

Heteronucl. NOE

49 NOE values in 1 lists
Value type peak integral, Field strength (¹H) 700.13 MHz, Pressure 1 atm, Temperature 298 K, pH 7.5 Detail

Heteronucl. T₁/T₂

49 T₁/T₂ values in 1 lists
Field strength (¹H) 700.13 MHz, Pressure 1 atm, Temperature 298 K, pH 7.5 Detail

Release date

2008-11-13

Citation

The copper-responsive repressor CopR of Lactococcus lactis is a 'winged helix' protein
Cantini, F., Banci, L., Solioz, M.
Biochem. J. (2009), 417, 493-499, PubMed 18837698 , DOI 10.1042/BJ20081713 , Abstract

Related entities 1. CopR-NTD, : 1 : 7 entities Detail

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	CopR-NTD	[U-99% 13C; U-99% 15N]		0.2 (±0.05) mM
2	NaPi			50 mM
3	NaCl			100 mM
4	H2O	natural abundance		90 %
5	D2O			10 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	CopR-NTD	[U-99% 13C; U-99% 15N]		0.2 (±0.05) mM
2	NaPi			50 mM
3	NaCl			100 mM
4	H2O	natural abundance		90 %
5	D2O			10 %

3 3D CBCA(CO)NH

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	CopR-NTD	[U-99% 13C; U-99% 15N]		0.2 (±0.05) mM
2	NaPi			50 mM
3	NaCl			100 mM
4	H2O	natural abundance		90 %
5	D2O			10 %

4 3D HNCO

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	CopR-NTD	[U-99% 13C; U-99% 15N]		0.2 (±0.05) mM
2	NaPi			50 mM
3	NaCl			100 mM
4	H2O	natural abundance		90 %
5	D2O			10 %

5 3D HNCA

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	CopR-NTD	[U-99% 13C; U-99% 15N]		0.2 (±0.05) mM
2	NaPi			50 mM
3	NaCl			100 mM
4	H2O	natural abundance		90 %
5	D2O			10 %

6 3D HNCACB

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	CopR-NTD	[U-99% 13C; U-99% 15N]		0.2 (±0.05) mM
2	NaPi			50 mM
3	NaCl			100 mM
4	H2O	natural abundance		90 %
5	D2O			10 %

7 3D HN(CO)CA

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	CopR-NTD	[U-99% 13C; U-99% 15N]		0.2 (±0.05) mM
2	NaPi			50 mM
3	NaCl			100 mM
4	H2O	natural abundance		90 %
5	D2O			10 %

8 3D 1H-15N NOESY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	CopR-NTD	[U-99% 13C; U-99% 15N]		0.2 (±0.05) mM
2	NaPi			50 mM
3	NaCl			100 mM
4	H2O	natural abundance		90 %
5	D2O			10 %

9 3D 1H-13C NOESY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	CopR-NTD	[U-99% 13C; U-99% 15N]		0.2 (±0.05) mM
2	NaPi			50 mM
3	NaCl			100 mM
4	H2O	natural abundance		90 %
5	D2O			10 %

10 3D HCCH-TOCSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	CopR-NTD	[U-99% 13C; U-99% 15N]		0.2 (±0.05) mM
2	NaPi			50 mM
3	NaCl			100 mM
4	H2O	natural abundance		90 %
5	D2O			10 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15793_2k4b.nef
Input source #2: Coordindates	2k4b.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---------
MSYYHHHHHHDYDIPTTENLYFQGAMNEVEFNVSNAELIVMRVIWSLGEARVDEIYAQIPQELEWSLATVKTLLGRLVKKEMLSTEKEGRKFVYRPLME
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MSYYHHHHHHDYDIPTTENLYFQGAMNEVEFNVSNAELIVMRVIWSLGEARVDEIYAQIPQELEWSLATVKTLLGRLVKKEMLSTEKEGRKFVYRPLME

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	99	0	0	100.0

Content subtype: combined_15793_2k4b.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	605		57.6 (chain: A, length: 99)
1	Distance restraints	AMBER_distance_constraints_3	OK	909 (1)	noe	56.6 (chain: A, length: 99)
1	Dihedral angle restraints	AMBER_dihedral_2	OK	94 (94)	.	61.6 (chain: A, length: 99)
2	Dihedral angle restraints	AMBER_dihedral_5	Warning	1 (1)	.	2.0 (chain: A, length: 99)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 99, Sequence coverage: 57.6%
- Total number of assignments
  - ¹H chemical shifts: 323
  - ¹³C chemical shifts: 230
  - ¹⁵N chemical shifts: 52
- 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

Distance restraints

Saveframe: AMBER_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 99, Sequence coverage: 56.6%
- Total number of restraints: 895
- Weight of restraints: 1.0 (895)
- Potential type of restraints: square-well-parabolic (895)
- Range of distance target values: 2.15, 4.38 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: AMBER_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 99, Sequence coverage: 61.6%
- Total number of restraints: 94
- Total number of restraints per polymer type: 94
- Weight of restraints: 1.0 (94)
- Potential type of restraints: square-well-parabolic (94)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
- Saveframe: AMBER_dihedral_5
  - Status: Warning
  - Experiment type: .
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 99, Sequence coverage: 2.0%
  - Total number of restraints: 1
  - Total number of restraints per polymer type: 1
  - Weight of restraints: 1.0 (1)
  - Potential type of restraints: square-well-parabolic (1)
  - Dihedral angle restraints per residue

Keywords DNA binding protein, Winged Helix