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- PDB-4lb6: Crystal structure of PKZ Zalpha in complex with ds(CG)6 (tetragon... -

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Basic information

Entry
Database: PDB / ID: 4lb6
TitleCrystal structure of PKZ Zalpha in complex with ds(CG)6 (tetragonal form)
Components
  • 5'-D(*TP*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*G)-3'
  • Protein kinase containing Z-DNA binding domains
KeywordsTRANSFERASE/DNA / wHTH / Zalpha / ZBD / Kinase / innate immunity / Z-DNA / Z-RNA / eIF2a / TRANSFERASE-DNA complex
Function / homology
Function and homology information


PKR-mediated signaling / left-handed Z-DNA binding / anatomical structure development / double-stranded RNA adenosine deaminase activity / eukaryotic translation initiation factor 2alpha kinase activity / defense response to virus / protein 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
DNA / DNA (> 10) / Interferon-induced, double-stranded RNA-activated protein kinase
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDe Rosa, M. / Zacarias, S. / Athanasiadis, A.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Structural basis for Z-DNA binding and stabilization by the zebrafish Z-DNA dependent protein kinase PKZ.
Authors: de Rosa, M. / Zacarias, S. / Athanasiadis, A.
History
DepositionJun 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Protein kinase containing Z-DNA binding domains
C: 5'-D(*TP*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*G)-3'


Theoretical massNumber of molelcules
Total (without water)12,4202
Polymers12,4202
Non-polymers00
Water1,31573
1
B: Protein kinase containing Z-DNA binding domains
C: 5'-D(*TP*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*G)-3'

B: Protein kinase containing Z-DNA binding domains
C: 5'-D(*TP*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*G)-3'

B: Protein kinase containing Z-DNA binding domains
C: 5'-D(*TP*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*G)-3'

B: Protein kinase containing Z-DNA binding domains
C: 5'-D(*TP*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*G)-3'


Theoretical massNumber of molelcules
Total (without water)49,6818
Polymers49,6818
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_556-y,-x,-z+11
crystal symmetry operation10_454-x-1/2,-y+1/2,z-1/21
crystal symmetry operation15_455y-1/2,x+1/2,-z+1/21
Buried area2800 Å2
ΔGint-25 kcal/mol
Surface area9050 Å2
Unit cell
Length a, b, c (Å)110.910, 110.910, 43.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11B-117-

HOH

21C-108-

HOH

31C-119-

HOH

41C-120-

HOH

51C-121-

HOH

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Components

#1: Protein Protein kinase containing Z-DNA binding domains / Uncharacterized protein / Z-DNA binding protein kinase


Mass: 8450.583 Da / Num. of mol.: 1 / Fragment: Zalpha domain, UNP residues 5-70
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: pkz / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q5NE14, non-specific serine/threonine protein kinase
#2: DNA chain 5'-D(*TP*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*G)-3'


Mass: 3969.561 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic oligonucleotide
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.67 Å3/Da / Density % sol: 53.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 2.0 M ammonium sulfate, 0.1 M sodium acetate, 7.5 % glycerol, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 70 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97 Å
DetectorType: PILATUS 6M-F / Detector: PIXEL / Date: Sep 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.8→32.55 Å / Num. obs: 12161 / % possible obs: 96.4 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Biso Wilson estimate: 27.1 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 11.3
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.679 / Mean I/σ(I) obs: 2.2 / % possible all: 96

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4LB5

4lb5


Resolution: 1.8→28.072 Å / SU ML: 0.17 / σ(F): 1.35 / Phase error: 21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2116 1216 10 %lattice symmetry 10%
Rwork0.1809 ---
obs0.1841 12155 94.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→28.072 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms535 123 0 73 731
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019684
X-RAY DIFFRACTIONf_angle_d2.062944
X-RAY DIFFRACTIONf_dihedral_angle_d19.133274
X-RAY DIFFRACTIONf_chiral_restr0.138105
X-RAY DIFFRACTIONf_plane_restr0.009100
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.87210.25741310.23281188X-RAY DIFFRACTION95
1.8721-1.95730.2511330.22371188X-RAY DIFFRACTION95
1.9573-2.06040.24361310.20191178X-RAY DIFFRACTION95
2.0604-2.18950.231350.18771213X-RAY DIFFRACTION96
2.1895-2.35840.21121350.17931211X-RAY DIFFRACTION96
2.3584-2.59560.22291360.18931231X-RAY DIFFRACTION97
2.5956-2.97090.21751380.19481241X-RAY DIFFRACTION97
2.9709-3.74160.21390.16621244X-RAY DIFFRACTION96
3.7416-28.07540.19391380.16671245X-RAY DIFFRACTION90
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.61311.8549-0.34185.9651-0.03472.0744-0.0160.2205-0.1579-0.3529-0.342-0.55630.1731.00050.29320.16150.0215-0.04580.56340.0690.392-4.64127.913420.4601
26.17642.54360.47557.4409-0.19375.3858-0.62241.70570.4543-0.7020.8746-0.2335-0.07560.553-0.14890.187-0.0467-0.03180.49170.04550.2409-13.053728.108714.8579
39.78030.8632.27429.11284.68712.83010.1051-0.58510.34940.39950.0212-0.2850.06870.0973-0.09380.1332-0.00460.0120.24620.02670.1799-15.136528.827125.6203
49.041-6.15772.0036.0914-1.50145.7413-0.0751-0.77261.5113-0.04790.68920.314-0.35470.656-0.47420.2292-0.0585-0.01250.4531-0.14310.8008-10.669438.250526.6675
51.88230.5101-0.92530.40330.96976.6748-0.4020.08611.9318-0.2186-0.16380.3378-1.1181-0.04050.57340.2992-0.0648-0.07730.25870.07610.8813-16.215939.695719.5571
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 7 through 21 )
2X-RAY DIFFRACTION2chain 'B' and (resid 22 through 36 )
3X-RAY DIFFRACTION3chain 'B' and (resid 37 through 49 )
4X-RAY DIFFRACTION4chain 'B' and (resid 50 through 56 )
5X-RAY DIFFRACTION5chain 'B' and (resid 57 through 69 )

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