BMRBj - BMREntryMaster

Found 1 Document (0.77 seconds)

BMRB: 30092

5JYU

NMR structure of pseudo receiver domain of CikA from Thermosynechococcus elongatus

Authors

Tseng, R.D., Wang, A.L.

Assembly

Two-component sensor histidine kinase

Entity

1. Two-component sensor histidine kinase (polymer, Thiol state: unknown), 117 monomers, 12891.67 Da Detail

EGRIVLVSED EATSTLICSI LTTAGYQVIW LVDGEVERLL ALTPIAVLLA EPFSYGDVQE LVDQLRQRCT PEQLKIFILG SKGNYQGVDR YIPLPIHPES FLQQVTMGLT SLATSAQ

Formula weight

12891.67 Da

Source organism

Thermosynechococcus vestitus BP-1

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 99.1 %, Completeness: 89.8 %, Completeness (bb): 98.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.8 % (1214 of 1352)	88.9 % (617 of 694)	90.7 % (486 of 536)	91.0 % (111 of 122)
Backbone	98.3 % (678 of 690)	98.3 % (232 of 236)	98.0 % (336 of 343)	99.1 % (110 of 111)
Sidechain	83.5 % (644 of 771)	84.1 % (385 of 458)	85.4 % (258 of 302)	9.1 % (1 of 11)
Aromatic	2.6 % (2 of 78)	2.6 % (1 of 39)	0.0 % (0 of 38)	100.0 % (1 of 1)
Methyl	97.7 % (172 of 176)	97.7 % (86 of 88)	97.7 % (86 of 88)

1. Two-component sensor histidine kinase

EGRIVLVSED EATSTLICSI LTTAGYQVIW LVDGEVERLL ALTPIAVLLA EPFSYGDVQE LVDQLRQRCT PEQLKIFILG SKGNYQGVDR YIPLPIHPES FLQQVTMGLT SLATSAQ

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 1500 uM [U-99% 13C; U-99% 15N] pseudo receiver domain of CikA, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	pseudo receiver domain of CikA	[U-99% 13C; U-99% 15N]	1500 uM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %

Sample #2

Solvent system 99.96% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 1500 uM [U-99% 13C; U-99% 15N] pseudo receiver domain of CikA, 99.96% D2O

#	Name	Isotope labeling	Concentration
4	pseudo receiver domain of CikA	[U-99% 13C; U-99% 15N]	1500 uM
5	H2O	natural abundance	0.04 %
6	D2O	natural abundance	99.96 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 300 uM [U-99% 13C; U-99% 15N] pseudo receiver domain of CikA, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
7	pseudo receiver domain of CikA	[U-99% 13C; U-99% 15N]	300 uM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

Sample #4

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 450 uM [U-99% 13C; U-99% 15N] pseudo receiver domain of CikA, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
10	pseudo receiver domain of CikA	[U-99% 13C; U-99% 15N]	450 uM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	601.13 MHz	internal	indirect	1.0

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	601.13 MHz	internal	indirect	1.0

Referencing offset: -0.01 ppm, Outliers: 3 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	601.13 MHz	internal	indirect	1.0

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	601.13 MHz	internal	indirect	1.0

Referencing offset: -0.01 ppm, Outliers: 3 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	601.13 MHz	internal	indirect	1.0

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	601.13 MHz	internal	indirect	1.0

Referencing offset: -0.07 ppm, Outliers: 2 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	601.13 MHz	internal	indirect	1.0

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	601.13 MHz	internal	indirect	1.0

Referencing offset: 0.11 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 5JYU, Strand ID: A Detail

Release date

2016-05-24

Citation

Structural basis of the day-night transition in a bacterial circadian clock
Tseng, R., Goularte, N.F., Chavan, A., Luu, J., Cohen, S.E., Chang, Y.G., Heisler, J., Li, S., Michael, A.K., Tripathi, S., Golden, S.S., LiWang, A., Partch, C.L.
Science (2017), 355, 1174-1180, PubMed 28302851 , DOI 10.1126/science.aag2516 , Abstract

Related entities 1. Two-component sensor histidine kinase, : 2 entities Detail

Experiments performed 15 experiments Detail

1 3D HNCACB

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 1500 uM [U-99% 13C; U-99% 15N] pseudo receiver domain of CikA, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	pseudo receiver domain of CikA	[U-99% 13C; U-99% 15N]	1500 uM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %

2 3D HN(CO)CACB

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 1500 uM [U-99% 13C; U-99% 15N] pseudo receiver domain of CikA, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	pseudo receiver domain of CikA	[U-99% 13C; U-99% 15N]	1500 uM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %

3 3D HNCO

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 1500 uM [U-99% 13C; U-99% 15N] pseudo receiver domain of CikA, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	pseudo receiver domain of CikA	[U-99% 13C; U-99% 15N]	1500 uM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %

4 3D HN(CA)CO

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 1500 uM [U-99% 13C; U-99% 15N] pseudo receiver domain of CikA, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	pseudo receiver domain of CikA	[U-99% 13C; U-99% 15N]	1500 uM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %

5 3D HBHA(CO)NH

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 1500 uM [U-99% 13C; U-99% 15N] pseudo receiver domain of CikA, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	pseudo receiver domain of CikA	[U-99% 13C; U-99% 15N]	1500 uM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %

6 3D IPAP-HNCO

Instrument

Bruker AvanceIII - 600 MHz

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 450 uM [U-99% 13C; U-99% 15N] pseudo receiver domain of CikA, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
10	pseudo receiver domain of CikA	[U-99% 13C; U-99% 15N]	450 uM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

7 3D IPAP-HNCO

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 300 uM [U-99% 13C; U-99% 15N] pseudo receiver domain of CikA, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
7	pseudo receiver domain of CikA	[U-99% 13C; U-99% 15N]	300 uM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

8 3D IPAP-HNCO(CA)

Instrument

Bruker AvanceIII - 600 MHz

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 450 uM [U-99% 13C; U-99% 15N] pseudo receiver domain of CikA, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
10	pseudo receiver domain of CikA	[U-99% 13C; U-99% 15N]	450 uM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

9 3D IPAP-HNCO(CA)

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 300 uM [U-99% 13C; U-99% 15N] pseudo receiver domain of CikA, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
7	pseudo receiver domain of CikA	[U-99% 13C; U-99% 15N]	300 uM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

10 3D HCCH-COSY

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 99.96% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 1500 uM [U-99% 13C; U-99% 15N] pseudo receiver domain of CikA, 99.96% D2O

#	Name	Isotope labeling	Concentration
4	pseudo receiver domain of CikA	[U-99% 13C; U-99% 15N]	1500 uM
5	H2O	natural abundance	0.04 %
6	D2O	natural abundance	99.96 %

11 3D 1H-13C NOESY

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 99.96% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 1500 uM [U-99% 13C; U-99% 15N] pseudo receiver domain of CikA, 99.96% D2O

#	Name	Isotope labeling	Concentration
4	pseudo receiver domain of CikA	[U-99% 13C; U-99% 15N]	1500 uM
5	H2O	natural abundance	0.04 %
6	D2O	natural abundance	99.96 %

12 3D 1H-15N NOESY

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 1500 uM [U-99% 13C; U-99% 15N] pseudo receiver domain of CikA, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	pseudo receiver domain of CikA	[U-99% 13C; U-99% 15N]	1500 uM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %

13 3D H(CCO)NH

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 1500 uM [U-99% 13C; U-99% 15N] pseudo receiver domain of CikA, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	pseudo receiver domain of CikA	[U-99% 13C; U-99% 15N]	1500 uM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %

14 2D 1H-15N HSQC

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 1500 uM [U-99% 13C; U-99% 15N] pseudo receiver domain of CikA, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	pseudo receiver domain of CikA	[U-99% 13C; U-99% 15N]	1500 uM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %

15 2D 1H-13C HSQC

Instrument

Bruker AvanceIII - 600 MHz

Sample

State isotropic, Solvent system 99.96% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 1500 uM [U-99% 13C; U-99% 15N] pseudo receiver domain of CikA, 99.96% D2O

#	Name	Isotope labeling	Concentration
4	pseudo receiver domain of CikA	[U-99% 13C; U-99% 15N]	1500 uM
5	H2O	natural abundance	0.04 %
6	D2O	natural abundance	99.96 %

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_30092_5jyu.nef
Input source #2: Coordindates	5jyu.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

-----620-------630-------640-------650-------660-------670-------680-------690-------700-------710--
EGRIVLVSEDEATSTLICSILTTAGYQVIWLVDGEVERLLALTPIAVLLAEPFSYGDVQELVDQLRQRCTPEQLKIFILGSKGNYQGVDRYIPLPIHPES
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
EGRIVLVSEDEATSTLICSILTTAGYQVIWLVDGEVERLLALTPIAVLLAEPFSYGDVQELVDQLRQRCTPEQLKIFILGSKGNYQGVDRYIPLPIHPES
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-----720---------
FLQQVTMGLTSLATSAQ
|||||||||||||||||
FLQQVTMGLTSLATSAQ
-------110-------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	117	0	0	100.0

Content subtype: combined_30092_5jyu.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1221		99.1 (chain: A, length: 117)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	5293 (1)	noe	99.1 (chain: A, length: 117)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	188 (188)	.	88.9 (chain: A, length: 117)
2	Dihedral angle restraints	CNS/XPLOR_dihedral_4	Warning	8 (8)	.	10.3 (chain: A, length: 117)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_5	OK	165 (165)	.	50.4 (chain: A, length: 117)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 117, Sequence coverage: 99.1%
- Total number of assignments
  - ¹H chemical shifts: 623
  - ¹³C chemical shifts: 488
  - ¹⁵N chemical shifts: 110
- 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	694	623	89.8
¹³C chemical shifts	536	488	91.0
¹⁵N chemical shifts	127	110	86.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	236	233	98.7
¹³C chemical shifts	234	230	98.3
¹⁵N chemical shifts	111	109	98.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	458	390	85.2
¹³C chemical shifts	302	258	85.4
¹⁵N chemical shifts	16	1	6.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	89	88	98.9
¹³C chemical shifts	89	86	96.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	39	1	2.6
¹³C chemical shifts	38	0	0.0
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: 117, Sequence coverage: 99.1%
- Total number of restraints: 4956
- Weight of restraints: 1.0 (4956)
- Potential type of restraints: square-well-parabolic (4956)
- Range of distance target values: 2.0, 5.25 (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: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 117, Sequence coverage: 88.9%
- Total number of restraints: 188
- Total number of restraints per polymer type: 188
- Weight of restraints: 1.0 (188)
- Potential type of restraints: square-well-parabolic (188)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
- Saveframe: CNS/XPLOR_dihedral_4
  - Status: Warning
  - Experiment type: .
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 117, Sequence coverage: 10.3%
  - Total number of restraints: 8
  - Total number of restraints per polymer type: 8
  - Weight of restraints: 1.0 (8)
  - Potential type of restraints: square-well-parabolic (8)
  - Plot of Phi-Psi angle restraints
  - Dihedral angle restraints per residue

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_5
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 117, Sequence coverage: 50.4%
- Total number of restraints: 165
- Potential type of restraints: square-well-parabolic (165)
- Range of observed RDC values: -33.6, 50.6 (Hz)
- Histogram of observed RDC values
- RDC restraints per residue
  - Chain_ID: A
    None

Keywords Circadian Clock, Signaling protein

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Found 1 Document (0.77 seconds)

BMRB: 30092

Sample #1

Sample #2

Sample #3

Sample #4

Chemical shift reference #1

Chemical shift reference #2

Chemical shift reference #1

Chemical shift reference #2

Chemical shift reference #1

Chemical shift reference #2

Chemical shift reference #1

Chemical shift reference #2

Related entities 1. Two-component sensor histidine kinase, : 2 entities Detail

Experiments performed 15 experiments Detail

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NMR combined restraints 6 contents Detail