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- PDB-4kmf: Crystal structure of Zalpha domain from Carassius auratus PKZ in ... -

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Basic information

Entry
Database: PDB / ID: 4kmf
TitleCrystal structure of Zalpha domain from Carassius auratus PKZ in complex with Z-DNA
Components
  • DNA (5'-D(*TP*CP*GP*CP*GP*CP*G)-3')
  • Interferon-inducible and double-stranded-dependent eIF-2kinase
KeywordsTRANSFERASE/DNA / Zalpha / Z-DNA / PKZ / goldfish / TRANSFERASE-DNA complex
Function / homology
Function and homology information


double-stranded RNA adenosine deaminase activity / protein kinase activity / RNA binding / ATP binding
Similarity search - Function
Z-DNA-binding domain in adenosine deaminases. / Z-binding domain / Adenosine deaminase z-alpha domain / Z-binding domain profile. / : / 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. ...Z-DNA-binding domain in adenosine deaminases. / Z-binding domain / Adenosine deaminase z-alpha domain / Z-binding domain profile. / : / 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
: / DNA / Interferon-inducible and double-stranded-dependent eIF-2kinase
Similarity search - Component
Biological speciesCarassius auratus (goldfish)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsKim, D. / Kim, K.K.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Distinct Z-DNA binding mode of a PKR-like protein kinase containing a Z-DNA binding domain (PKZ).
Authors: Kim, D. / Hur, J. / Park, K. / Bae, S. / Shin, D. / Ha, S.C. / Hwang, H.Y. / Hohng, S. / Lee, J.H. / Lee, S. / Kim, Y.G. / Kim, K.K.
History
DepositionMay 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Source and taxonomy / Category: pdbx_entity_src_syn / software
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _software.name
Revision 1.3Jan 29, 2020Group: Derived calculations
Category: ndb_struct_na_base_pair_step / pdbx_struct_assembly ...ndb_struct_na_base_pair_step / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _ndb_struct_na_base_pair_step.inclination
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interferon-inducible and double-stranded-dependent eIF-2kinase
B: DNA (5'-D(*TP*CP*GP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3683
Polymers9,3132
Non-polymers551
Water1,26170
1
A: Interferon-inducible and double-stranded-dependent eIF-2kinase
B: DNA (5'-D(*TP*CP*GP*CP*GP*CP*G)-3')
hetero molecules

A: Interferon-inducible and double-stranded-dependent eIF-2kinase
B: DNA (5'-D(*TP*CP*GP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7356
Polymers18,6254
Non-polymers1102
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area2420 Å2
ΔGint-30 kcal/mol
Surface area9490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.367, 49.471, 29.585
Angle α, β, γ (deg.)90.000, 97.220, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 7198.205 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: codon optimized / Source: (gene. exp.) Carassius auratus (goldfish) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7T2M9
#2: DNA chain DNA (5'-D(*TP*CP*GP*CP*GP*CP*G)-3')


Mass: 2114.398 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic oligonucleotide / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.01 %
Crystal growTemperature: 295 K / Method: vapor diffusion
Details: 30% PEG1500, 15 mM MnCl2, vapor diffusion, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 23, 2006
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 8549 / % possible obs: 97.5 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.061 / Χ2: 3.175 / Net I/σ(I): 15.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.7-1.7330.3253991.802189.9
1.73-1.763.20.2724071.892194.9
1.76-1.793.30.2464151.879196.5
1.79-1.833.40.2174342.052199.3
1.83-1.873.50.1824392.1631100
1.87-1.913.60.1664272.486199.8
1.91-1.963.70.1474442.2671100
1.96-2.023.60.1334272.491199.8
2.02-2.073.70.1164442.7151100
2.07-2.143.60.1094433.019199.8
2.14-2.223.70.0954213.171100
2.22-2.313.60.094483.4571100
2.31-2.413.60.0884283.6071100
2.41-2.543.60.0824303.8211100
2.54-2.73.60.0764533.77199.6
2.7-2.913.50.0714394.39199.5
2.91-3.23.10.0434244.759197
3.2-3.662.90.0374124.762193.4
3.66-4.612.80.0344025.1190.5
4.61-502.80.0354135.115190

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.11data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→27.46 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.954 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 4.84 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.184 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2269 404 4.7 %RANDOM
Rwork0.1704 ---
obs0.1729 8535 97.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 57.77 Å2 / Biso mean: 24.5162 Å2 / Biso min: 13.47 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20.01 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.7→27.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms490 139 1 70 700
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022652
X-RAY DIFFRACTIONr_angle_refined_deg1.6022.226909
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.686561
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.83825.41724
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.3051592
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.651153
X-RAY DIFFRACTIONr_chiral_restr0.10.2104
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021442
X-RAY DIFFRACTIONr_mcbond_it1.2811.5309
X-RAY DIFFRACTIONr_mcangle_it2.2442498
X-RAY DIFFRACTIONr_scbond_it3.7343343
X-RAY DIFFRACTIONr_scangle_it5.254.5411
X-RAY DIFFRACTIONr_rigid_bond_restr2.0443652
LS refinement shellResolution: 1.702→1.746 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 29 -
Rwork0.223 567 -
all-596 -
obs--91.41 %

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