[English] 日本語
Yorodumi
- PDB-4dgm: Crystal Structure of maize CK2 in complex with the inhibitor apigenin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4dgm
TitleCrystal Structure of maize CK2 in complex with the inhibitor apigenin
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / protein kinase / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


regulation of transcription by RNA polymerase I / regulation of transcription by RNA polymerase III / protein kinase CK2 complex / non-specific serine/threonine protein kinase / regulation of cell cycle / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / ATP binding ...regulation of transcription by RNA polymerase I / regulation of transcription by RNA polymerase III / protein kinase CK2 complex / non-specific serine/threonine protein kinase / regulation of cell cycle / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / ATP binding / nucleus / cytosol
Similarity search - Function
Casein Kinase 2, subunit alpha / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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
Chem-AGI / DI(HYDROXYETHYL)ETHER / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsLolli, G. / Mazzorana, M. / Battistutta, R.
CitationJournal: Biochemistry / Year: 2012
Title: Inhibition of protein kinase CK2 by flavonoids and tyrphostins. A structural insight.
Authors: Lolli, G. / Cozza, G. / Mazzorana, M. / Tibaldi, E. / Cesaro, L. / Donella-Deana, A. / Meggio, F. / Venerando, A. / Franchin, C. / Sarno, S. / Battistutta, R. / Pinna, L.A.
History
DepositionJan 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2012Group: Database references
Revision 1.2Jan 2, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Casein kinase II subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2397
Polymers38,6141
Non-polymers6256
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)142.363, 59.875, 45.931
Angle α, β, γ (deg.)90.000, 103.400, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Casein kinase II subunit alpha / CK II / CK2-alpha


Mass: 38614.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: ACK2 / Production host: Escherichia coli (E. coli)
References: UniProt: P28523, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-AGI / 5,7-dihydroxy-2-(4-hydroxyphenyl)-4H-chromen-4-one / Apigenin


Mass: 270.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H10O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.47 Å3/Da / Density % sol: 50.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: 0.1 M Tris-HCl, 10-20% PEG 4000, 0.2 M Na-acetate, pH 8, VAPOR DIFFUSION, temperature 293K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.65→69.242 Å / Num. all: 45035 / Num. obs: 45035 / % possible obs: 99.5 % / Redundancy: 4 % / Rsym value: 0.062 / Net I/σ(I): 11.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.65-1.7440.4462.32638965400.446100
1.74-1.844.10.263.82541562690.2699.9
1.84-1.9740.1895.82354358410.18999.9
1.97-2.134.10.0939.22217054720.09399.9
2.13-2.3340.08112.21995750000.08199.9
2.33-2.6140.05516.11834045550.05599.9
2.61-3.0140.05419.81605040380.05499.9
3.01-3.693.80.04824.51299633880.04899.7
3.69-5.223.70.05127954926000.05198.2
5.22-54.9583.70.05126.3492013320.05189.4

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.20data scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→69.242 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.937 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.599 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.023 / ESU R Free: 0.024 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.252 2263 5 %RANDOM
Rwork0.2115 ---
obs0.2135 45014 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 71.39 Å2 / Biso mean: 37.2136 Å2 / Biso min: 17.27 Å2
Baniso -1Baniso -2Baniso -3
1--0.91 Å20 Å2-18.85 Å2
2---17.84 Å2-0 Å2
3---18.75 Å2
Refinement stepCycle: LAST / Resolution: 1.65→69.242 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2723 0 43 165 2931
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022865
X-RAY DIFFRACTIONr_angle_refined_deg1.3621.973874
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2545337
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.07123.986148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.05315516
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5531519
X-RAY DIFFRACTIONr_chiral_restr0.0920.2406
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212187
LS refinement shellResolution: 1.649→1.692 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 153 -
Rwork0.359 3122 -
all-3275 -
obs--98.7 %
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)
12.60671.22771.33841.44370.04962.268-0.12970.1622-0.07160.06880.075-0.2963-0.32780.21150.05480.06480.009-0.01750.2222-0.07730.198521.81097.820311.1476
22.2910.7211-0.04222.9735-0.95922.60850.0975-0.0407-0.58060.10620.1754-0.69620.3970.2487-0.27280.09280.0537-0.14250.2643-0.12850.396917.636-13.62139.1484
31.2617-0.7013-0.45213.35650.40073.2237-0.14610.0029-0.58830.0050.21660.00420.5762-0.0708-0.07050.26110.0032-0.1290.3647-0.06060.501111.5598-21.32129.8579
46.4504-1.6651-0.68213.57840.12373.44920.0402-0.0339-0.32940.08020.3279-0.01010.1283-0.2281-0.36810.0173-0.0038-0.03930.26350.00660.10752.6265-6.17966.2386
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 184
2X-RAY DIFFRACTION2A185 - 256
3X-RAY DIFFRACTION3A257 - 294
4X-RAY DIFFRACTION4A295 - 331

+
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://pdbjlvh1.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