BMRBj - BMREntryMaster

	Total	¹H	¹³C	¹⁵N
All	72.8 % (552 of 758)	77.1 % (310 of 402)	62.9 % (180 of 286)	88.6 % (62 of 70)
Backbone	82.6 % (322 of 390)	95.4 % (125 of 131)	68.9 % (135 of 196)	98.4 % (62 of 63)
Sidechain	68.1 % (294 of 432)	68.3 % (185 of 271)	70.8 % (109 of 154)	0.0 % (0 of 7)
Aromatic	25.0 % (2 of 8)	50.0 % (2 of 4)	0.0 % (0 of 4)
Methyl	92.9 % (65 of 70)	91.4 % (32 of 35)	94.3 % (33 of 35)

1. CytR DBD

KAKKQETAAT MKDVALKAKV STATVSRALM NPDKVSQATR NRVEKAAREV GYLPQPMGRN VKRNES

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.0, Details 0.411 MM [U-15N] CYTR DBD, 1.14 MM ATTTATGCAACGCA DNA, 50 MM SODIUM PHOSPHATE, 30 MM SODIUM CHLORIDE, 1 MM EDTA, 90% H2O/10 D2O

#	Name	Isotope labeling	Concentration
1	HTH-TYPE TRANSCRIPTIONAL REPRESSOR CYTR	[U-15N]	0.411 mM
2	ATTTATGCAACGCA DNA	natural abundance	1.14 mM
3	sodium phosphate	natural abundance	50 mM
4	sodium chloride	natural abundance	30 mM
5	EDTA	natural abundance	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.0

#	Name	Isotope labeling	Concentration
8	HTH-TYPE TRANSCRIPTIONAL REPRESSOR CYTR	[U-13C; U-15N]	1 mM
9	ATTTATGCAACGCA DNA	natural abundance	1.2 mM
10	sodium phosphate	natural abundance	50 mM
11	sodium chloride	natural abundance	30 mM
12	EDTA	natural abundance	1 mM
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.0, Details 0.4 MM [U-15N] CYT DBD, 0.6 MM ATTTATGCAACGCA DNA, 50 MM SODIUM PHOSPHATE, 30 MM SODIUM CHLORIDE, 1 MM EDTA, 4 % C12E5 PEG/HEXANOL, 90% H2O/10%

#	Name	Isotope labeling	Concentration
15	HTH-TYPE TRANSCRIPTIONAL REPRESSOR CYTR	[U-15N]	0.4 mM
16	ATTTATGCAACGCA DNA	natural abundance	0.6 mM
17	sodium phosphate	natural abundance	50 mM
18	sodium chloride	natural abundance	30 mM
19	EDTA	natural abundance	1 mM
20	C12E5 PEG/HEXANOL	natural abundance	4 %
21	H2O	natural abundance	90 %
22	D2O	natural abundance	10 %

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: -0.36 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: -0.36 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: -0.06 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 11 models in PDB: 2LCV, Strand ID: A Detail

Release date

2011-06-21

Citation

Multiple conformations of the cytidine repressor DNA-binding domain coalesce to one upon recognition of a specific DNA surface
Moody, C.L., Tretyachenko-Ladokhina, V., Laue, T.M., Senear, D.F., Cocco, M.J.
Biochemistry (2011), 50, 6622-6632, PubMed 21688840 , DOI 10.1021/bi200205v , Abstract

Related entities 1. Cytidine Repressor DNA-Binding Domain, : 1 : 3 : 121 entities Detail

Experiments performed 8 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.0, Details 0.411 MM [U-15N] CYTR DBD, 1.14 MM ATTTATGCAACGCA DNA, 50 MM SODIUM PHOSPHATE, 30 MM SODIUM CHLORIDE, 1 MM EDTA, 90% H2O/10 D2O

#	Name	Isotope labeling	Concentration
1	HTH-TYPE TRANSCRIPTIONAL REPRESSOR CYTR	[U-15N]	0.411 mM
2	ATTTATGCAACGCA DNA	natural abundance	1.14 mM
3	sodium phosphate	natural abundance	50 mM
4	sodium chloride	natural abundance	30 mM
5	EDTA	natural abundance	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

2 3D HNCACB

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.0

#	Name	Isotope labeling	Concentration
8	HTH-TYPE TRANSCRIPTIONAL REPRESSOR CYTR	[U-13C; U-15N]	1 mM
9	ATTTATGCAACGCA DNA	natural abundance	1.2 mM
10	sodium phosphate	natural abundance	50 mM
11	sodium chloride	natural abundance	30 mM
12	EDTA	natural abundance	1 mM
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

3 3D CBCA(CO)NH

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.0

#	Name	Isotope labeling	Concentration
8	HTH-TYPE TRANSCRIPTIONAL REPRESSOR CYTR	[U-13C; U-15N]	1 mM
9	ATTTATGCAACGCA DNA	natural abundance	1.2 mM
10	sodium phosphate	natural abundance	50 mM
11	sodium chloride	natural abundance	30 mM
12	EDTA	natural abundance	1 mM
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

4 3D 1H-15N NOESY

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	HTH-TYPE TRANSCRIPTIONAL REPRESSOR CYTR	[U-15N]	0.411 mM
2	ATTTATGCAACGCA DNA	natural abundance	1.14 mM
3	sodium phosphate	natural abundance	50 mM
4	sodium chloride	natural abundance	30 mM
5	EDTA	natural abundance	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

5 3D 1H-15N TOCSY

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	HTH-TYPE TRANSCRIPTIONAL REPRESSOR CYTR	[U-15N]	0.411 mM
2	ATTTATGCAACGCA DNA	natural abundance	1.14 mM
3	sodium phosphate	natural abundance	50 mM
4	sodium chloride	natural abundance	30 mM
5	EDTA	natural abundance	1 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

6 3D 1H-13C NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.0

#	Name	Isotope labeling	Concentration
8	HTH-TYPE TRANSCRIPTIONAL REPRESSOR CYTR	[U-13C; U-15N]	1 mM
9	ATTTATGCAACGCA DNA	natural abundance	1.2 mM
10	sodium phosphate	natural abundance	50 mM
11	sodium chloride	natural abundance	30 mM
12	EDTA	natural abundance	1 mM
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

7 HCCH-TOCSY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.0

#	Name	Isotope labeling	Concentration
8	HTH-TYPE TRANSCRIPTIONAL REPRESSOR CYTR	[U-13C; U-15N]	1 mM
9	ATTTATGCAACGCA DNA	natural abundance	1.2 mM
10	sodium phosphate	natural abundance	50 mM
11	sodium chloride	natural abundance	30 mM
12	EDTA	natural abundance	1 mM
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

8 2D 1H-15N HSQC

Instrument

Varian INOVA - 800 MHz

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 0.4 MM [U-15N] CYT DBD, 0.6 MM ATTTATGCAACGCA DNA, 50 MM SODIUM PHOSPHATE, 30 MM SODIUM CHLORIDE, 1 MM EDTA, 4 % C12E5 PEG/HEXANOL, 90% H2O/10%

#	Name	Isotope labeling	Concentration
15	HTH-TYPE TRANSCRIPTIONAL REPRESSOR CYTR	[U-15N]	0.4 mM
16	ATTTATGCAACGCA DNA	natural abundance	0.6 mM
17	sodium phosphate	natural abundance	50 mM
18	sodium chloride	natural abundance	30 mM
19	EDTA	natural abundance	1 mM
20	C12E5 PEG/HEXANOL	natural abundance	4 %
21	H2O	natural abundance	90 %
22	D2O	natural abundance	10 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_17634_2lcv.nef
Input source #2: Coordindates	2lcv.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-------
MKAKKQETAATMKDVALKAKVSTATVSRALMNPDKVSQATRNRVEKAAREVGYLPQPMGRNVKRNES
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MKAKKQETAATMKDVALKAKVSTATVSRALMNPDKVSQATRNRVEKAAREVGYLPQPMGRNVKRNES

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	67	0	0	100.0

Content subtype: combined_17634_2lcv.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	535		98.5 (chain: A, length: 67)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	786 (1)	noe	70.1 (chain: A, length: 67)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 67, Sequence coverage: 98.5%
- Total number of assignments
  - ¹³C chemical shifts: 169
  - ¹H chemical shifts: 304
  - ¹⁵N chemical shifts: 62
- 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 (%)
¹³C chemical shifts	291	169	58.1
¹H chemical shifts	409	304	74.3
¹⁵N chemical shifts	77	62	80.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	134	66	49.3
¹H chemical shifts	133	125	94.0
¹⁵N chemical shifts	64	62	96.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	157	103	65.6
¹H chemical shifts	276	179	64.9
¹⁵N chemical shifts	13	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	39	34	87.2
¹H chemical shifts	39	34	87.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	4	0	0.0
¹H chemical shifts	4	2	50.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 67, Sequence coverage: 70.1%
- Total number of restraints: 786
- Weight of restraints: 1.0 (786)
- Potential type of restraints: square-well-parabolic (786)
- Range of distance target values: 2.1, 5.6 (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

Keywords BACTERIAL GENE REPRESSOR, CYTIDINE REPRESSOR, CYTR, DNA-BINDING, DNA BINDING PROTEI, HELIX TURN HEL BINDING DOMAIN, LACR FAMILY, REPRESSOR, TRANSCRIPTION, TRANSCRIPTION REGULATION

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Found 1 Document (0.832 seconds)

BMRB: 17634

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Cytidine Repressor DNA-Binding Domain, : 1 : 3 : 121 entities Detail

Experiments performed 8 experiments Detail

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Sample

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Sample

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Sample

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NMR combined restraints 3 contents Detail