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- PDB-2rvc: Solution structure of Zalpha domain of goldfish ZBP-containing pr... -

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Basic information

Entry
Database: PDB / ID: 2rvc
TitleSolution structure of Zalpha domain of goldfish ZBP-containing protein kinase
ComponentsInterferon-inducible and double-stranded-dependent eIF-2kinase
KeywordsDNA BINDING PROTEIN / Z dna binding protein / helix turn helix
Function / homology
Function and homology information


double-stranded RNA adenosine deaminase activity / eukaryotic translation initiation factor 2alpha kinase activity / RNA binding / ATP binding / nucleus / cytoplasm
Similarity search - Function
Z-DNA-binding domain in adenosine deaminases. / Z-binding domain profile. / Z-binding domain / Adenosine deaminase z-alpha domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Winged helix-like DNA-binding domain superfamily ...Z-DNA-binding domain in adenosine deaminases. / Z-binding domain profile. / Z-binding domain / Adenosine deaminase z-alpha domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Winged helix-like DNA-binding domain superfamily / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Interferon-inducible and double-stranded-dependent eIF-2kinase
Similarity search - Component
Biological speciesCarassius auratus (goldfish)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model1
AuthorsLee, A. / Park, C. / Park, J. / Kwon, M. / Choi, Y. / Kim, K. / Choi, B. / Lee, J.
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: 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.
Authors: Lee, A.R. / Park, C.J. / Cheong, H.K. / Ryu, K.S. / Park, J.W. / Kwon, M.Y. / Lee, J. / Kim, K.K. / Choi, B.S. / Lee, J.H.
History
DepositionJul 8, 2015Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Interferon-inducible and double-stranded-dependent eIF-2kinase


Theoretical massNumber of molelcules
Total (without water)7,4591
Polymers7,4591
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Interferon-inducible and double-stranded-dependent eIF-2kinase


Mass: 7458.514 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-64
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carassius auratus (goldfish) / Production host: Escherichia coli (E. coli) / References: UniProt: Q7T2M9

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D HNCA
1613D HBHA(CO)NH
1713D 1H-15N NOESY
1813D (H)CCH-TOCSY
1913D 1H-13C NOESY

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Sample preparation

DetailsContents: 1.0 mM [U-99% 13C; U-99% 15N] caZapkz-1, 100 mM sodium chloride-2, 10 mM sodium phosphate-3, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMcaZapkz-1[U-99% 13C; U-99% 15N]1
100 mMsodium chloride-21
10 mMsodium phosphate-31
Sample conditionsIonic strength: 0.1 / pH: 6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian Agilent DD2 / Manufacturer: Varian / Model: Agilent DD2 / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: CNS 1.3 in explicit solvent using the RECOORD protocol
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10 / Representative conformer: 1

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