[English] 日本語
Yorodumi
- PDB-4lb6: Crystal structure of PKZ Zalpha in complex with ds(CG)6 (tetragon... -

+
Open data


ID or keywords:

Loading...

-
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


left-handed Z-DNA binding / double-stranded RNA adenosine deaminase activity / eukaryotic translation initiation factor 2alpha kinase activity / protein kinase activity / RNA binding / ATP binding / nucleus / cytoplasm
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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more