[English] 日本語
Yorodumi
- PDB-6xx6: Arabidopsis thaliana Casein Kinase 2 (CK2) alpha-1 crystal form I -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6xx6
TitleArabidopsis thaliana Casein Kinase 2 (CK2) alpha-1 crystal form I
ComponentsCasein kinase II subunit alpha-1
KeywordsCELL CYCLE / Kinase / CK2 / Casein Kinase / PLANT PROTEIN
Function / homology
Function and homology information


protein kinase CK2 complex / regulation of circadian rhythm / kinase activity / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / nucleolus / ATP binding / nucleus
Similarity search - Function
Casein Kinase 2, subunit alpha / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site ...Casein Kinase 2, subunit alpha / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / PIVALIC ACID / Casein kinase II subunit alpha-1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84919690899 Å
AuthorsDemulder, M. / De Veylder, L. / Loris, R.
Funding support Belgium, 2items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)G023616N Belgium
Research Foundation - Flanders (FWO)G011420N Belgium
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2020
Title: Crystal structure of Arabidopsis thaliana casein kinase 2 alpha 1.
Authors: Demulder, M. / De Veylder, L. / Loris, R.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Demulder, M. / De Veylder, L. / Loris, R.
History
DepositionJan 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Casein kinase II subunit alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9416
Polymers40,5221
Non-polymers4195
Water6,359353
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-24 kcal/mol
Surface area15280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.98, 61.98, 227.73
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Casein kinase II subunit alpha-1 / CK II / Casein kinase alpha 1 / AtCKA1


Mass: 40521.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CKA1, At5g67380, K8K14.10 / Production host: Escherichia coli (E. coli)
References: UniProt: Q08467, non-specific serine/threonine protein kinase

-
Non-polymers , 5 types, 358 molecules

#2: Chemical ChemComp-PIV / PIVALIC ACID


Type: L-peptide linking / Mass: 102.132 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M sodium sulfate 0.1M Bis-Tris propane pH 6.5 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Apr 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.849→50 Å / Num. obs: 38648 / % possible obs: 98.7 % / Redundancy: 8.4 % / Biso Wilson estimate: 29.0568885607 Å2 / CC1/2: 0.998 / Net I/σ(I): 13.4
Reflection shellResolution: 1.85→1.96 Å / Num. unique obs: 5815 / CC1/2: 0.704

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PHASER1.11.1_2575phasing
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PZH

3pzh


Resolution: 1.84919690899→48.0095807101 Å / SU ML: 0.245576210565 / Cross valid method: FREE R-VALUE / σ(F): 1.362077121 / Phase error: 20.1312265863
RfactorNum. reflection% reflection
Rfree0.19905896854 3565 5.0086404316 %
Rwork0.173132304507 --
obs0.174441353737 35083 98.2469943545 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 33.560177005 Å2
Refinement stepCycle: LAST / Resolution: 1.84919690899→48.0095807101 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2696 0 20 353 3069
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006216939424452894
X-RAY DIFFRACTIONf_angle_d1.065092349813946
X-RAY DIFFRACTIONf_chiral_restr0.0399856326859425
X-RAY DIFFRACTIONf_plane_restr0.00435168801712506
X-RAY DIFFRACTIONf_dihedral_angle_d13.2818014091114
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8492-1.87450.4019985125311190.3661497646192252X-RAY DIFFRACTION81.5337001376
1.8745-1.90130.3401986348441310.3264792153432487X-RAY DIFFRACTION91.2831241283
1.9013-1.92970.3171469532741410.3097839717892653X-RAY DIFFRACTION95.717711545
1.9297-1.95980.300038439331380.2868203970892642X-RAY DIFFRACTION96.1272475795
1.9598-1.9920.3123737084971420.2697713869282675X-RAY DIFFRACTION96.6712422787
1.992-2.02630.2673720082331390.2443263517562698X-RAY DIFFRACTION98.4044398196
2.0263-2.06320.2306569475111460.2246780078882728X-RAY DIFFRACTION98.6273164036
2.0632-2.10290.2250556135151450.2020502052262693X-RAY DIFFRACTION99.3349667483
2.1029-2.14580.221096247231470.1929937867362778X-RAY DIFFRACTION99.6592844974
2.1458-2.19240.2475912192471420.1910413576442740X-RAY DIFFRACTION99.8613998614
2.1924-2.24340.2191385175871460.1890879091042735X-RAY DIFFRACTION99.9653018737
2.2434-2.29950.1901469649461530.1740621794072786X-RAY DIFFRACTION99.9319959198
2.2995-2.36170.2271747787991470.1766216448152727X-RAY DIFFRACTION99.8957247132
2.3617-2.43120.2216388062981440.1556802430162764X-RAY DIFFRACTION99.9656239257
2.4312-2.50970.1934237211961500.157512146672748X-RAY DIFFRACTION100
2.5097-2.59940.1880007769831350.1581013270192739X-RAY DIFFRACTION100
2.5994-2.70340.2048206191091460.1720334421392772X-RAY DIFFRACTION100
2.7034-2.82650.1877017955531480.1760272459072763X-RAY DIFFRACTION99.8970487303
2.8265-2.97550.2073935027921440.1780963596462722X-RAY DIFFRACTION100
2.9755-3.16180.2049436099371430.1718936035722754X-RAY DIFFRACTION100
3.1618-3.40590.1612119952361450.1655917134122741X-RAY DIFFRACTION99.9653619674
3.4059-3.74850.1824226628441460.1539869463162763X-RAY DIFFRACTION100
3.7485-4.29070.1690744455761400.1350122210842740X-RAY DIFFRACTION100
4.2907-5.40460.1526509599821430.1335192117772767X-RAY DIFFRACTION99.9656475438
5.4046-48.009580.1923969670021450.1704214506032745X-RAY DIFFRACTION99.4494150034

+
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