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BMRB: 11595

2RVC

Solution structure of Zalpha domain of goldfish ZBP-containing protein kinase

Authors

Lee, A., Park, C., Park, J., Kwon, M., Choi, Y., Kim, K., Choi, B., LEE, J.

Assembly

Zalpha domain

Entity

1. Zalpha domain (polymer, Thiol state: not present), 64 monomers, 7448.430 Da Detail

MSAETQMERK IIDFLRQNGK SIALTIAKEI GLDKSTVNRH LYNLQRSNQV FNSNEKPPVW DLME

Formula weight

7448.43 Da

Source organism

Carassius auratus

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 95.3 %, Completeness: 77.9 %, Completeness (bb): 81.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	77.9 % (608 of 780)	86.9 % (358 of 412)	61.0 % (180 of 295)	95.9 % (70 of 73)
Backbone	81.1 % (308 of 380)	95.3 % (122 of 128)	66.8 % (127 of 190)	95.2 % (59 of 62)
Sidechain	77.7 % (359 of 462)	83.1 % (236 of 284)	67.1 % (112 of 167)	100.0 % (11 of 11)
Aromatic	31.8 % (14 of 44)	59.1 % (13 of 22)	0.0 % (0 of 21)	100.0 % (1 of 1)
Methyl	83.8 % (57 of 68)	94.1 % (32 of 34)	73.5 % (25 of 34)

1. entity

MSAETQMERK IIDFLRQNGK SIALTIAKEI GLDKSTVNRH LYNLQRSNQV FNSNEKPPVW DLME

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	caZapkz	[U-99% 13C; U-99% 15N]	protein	1.0 mM
2	sodium chloride	natural abundance	salt	100 mM
3	sodium phosphate	natural abundance	buffer	10 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

LACS Plot; CA

Referencing offset: -0.56 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.56 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.0 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2RVC, Strand ID: A Detail

Release date

2016-01-31

Citation

Solution structure of the Z-DNA binding domain of PKR-like protein kinase from Carassius auratus and quantitative analyses of the intermediate complex during B-Z transition
Lee, A., Park, C., Park, J., Kwon, M., Choi, Y., Kim, K., Choi, B., Lee, J.
Nucleic Acids Res. (2016), PubMed 26792893 , DOI 10.1093/nar/gkw025 , Abstract

Related entities 1. Zalpha domain, : 1 : 1 : 61 entities Detail

Experiments performed 9 experiments Detail

1 2D 1H-15N HSQC

Instrument

Agilent DD2 - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	caZapkz	[U-99% 13C; U-99% 15N]	protein	1.0 mM
2	sodium chloride	natural abundance	salt	100 mM
3	sodium phosphate	natural abundance	buffer	10 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

2 3D HNCO

Instrument

Agilent DD2 - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	caZapkz	[U-99% 13C; U-99% 15N]	protein	1.0 mM
2	sodium chloride	natural abundance	salt	100 mM
3	sodium phosphate	natural abundance	buffer	10 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

3 3D CBCA(CO)NH

Instrument

Agilent DD2 - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	caZapkz	[U-99% 13C; U-99% 15N]	protein	1.0 mM
2	sodium chloride	natural abundance	salt	100 mM
3	sodium phosphate	natural abundance	buffer	10 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

4 3D HNCACB

Instrument

Agilent DD2 - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	caZapkz	[U-99% 13C; U-99% 15N]	protein	1.0 mM
2	sodium chloride	natural abundance	salt	100 mM
3	sodium phosphate	natural abundance	buffer	10 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

5 3D HNCA

Instrument

Agilent DD2 - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	caZapkz	[U-99% 13C; U-99% 15N]	protein	1.0 mM
2	sodium chloride	natural abundance	salt	100 mM
3	sodium phosphate	natural abundance	buffer	10 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

6 3D HBHA(CO)NH

Instrument

Agilent DD2 - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	caZapkz	[U-99% 13C; U-99% 15N]	protein	1.0 mM
2	sodium chloride	natural abundance	salt	100 mM
3	sodium phosphate	natural abundance	buffer	10 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

7 3D 1H-15N NOESY

Instrument

Agilent DD2 - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	caZapkz	[U-99% 13C; U-99% 15N]	protein	1.0 mM
2	sodium chloride	natural abundance	salt	100 mM
3	sodium phosphate	natural abundance	buffer	10 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

8 3D HCCH-TOCSY

Instrument

Agilent DD2 - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	caZapkz	[U-99% 13C; U-99% 15N]	protein	1.0 mM
2	sodium chloride	natural abundance	salt	100 mM
3	sodium phosphate	natural abundance	buffer	10 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

9 3D 1H-13C NOESY

Instrument

Agilent DD2 - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	caZapkz	[U-99% 13C; U-99% 15N]	protein	1.0 mM
2	sodium chloride	natural abundance	salt	100 mM
3	sodium phosphate	natural abundance	buffer	10 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_11595_2rvc.nef
Input source #2: Coordindates	2rvc.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----
MSAETQMERKIIDFLRQNGKSIALTIAKEIGLDKSTVNRHLYNLQRSNQVFNSNEKPPVWDLME
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MSAETQMERKIIDFLRQNGKSIALTIAKEIGLDKSTVNRHLYNLQRSNQVFNSNEKPPVWDLME

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	64	0	0	100.0

Content subtype: combined_11595_2rvc.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	587		95.3 (chain: A, length: 64)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	1108 (1)	noe	93.8 (chain: A, length: 64)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	109 (109)	.	92.2 (chain: A, length: 64)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 64, Sequence coverage: 95.3%
- Total number of assignments
  - ¹H chemical shifts: 348
  - ¹³C chemical shifts: 169
  - ¹⁵N chemical shifts: 70
- 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: CNS/XPLOR_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 64, Sequence coverage: 93.8%
- Total number of restraints: 1108
- Weight of restraints: 1.0 (1108)
- Potential type of restraints: square-well-parabolic (1108)
- Range of distance target values: 2.13, 3.9 (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_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 64, Sequence coverage: 92.2%
- Total number of restraints: 109
- Total number of restraints per polymer type: 109
- Weight of restraints: 1.0 (109)
- Potential type of restraints: square-well-parabolic (109)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Z dna binding protein, helix turn helix