[English] 日本語
Yorodumi
- PDB-3pwd: Crystal structure of maize CK2 in complex with NBC (Z1) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3pwd
TitleCrystal structure of maize CK2 in complex with NBC (Z1)
ComponentsCasein kinase II subunit alpha
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / protein kinase / inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


protein kinase CK2 complex / non-specific serine/threonine protein kinase / regulation of cell cycle / protein serine kinase activity / protein serine/threonine kinase activity / 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-CZ0 / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Rigid body / Resolution: 2.2 Å
AuthorsBattistutta, R. / Mazzorana, M.
CitationJournal: Cell.Mol.Life Sci. / Year: 2012
Title: Structural features underlying the selectivity of the kinase inhibitors NBC and dNBC: role of a nitro group that discriminates between CK2 and DYRK1A
Authors: Sarno, S. / Mazzorana, M. / Traynor, R. / Ruzzene, M. / Cozza, G. / Pagano, M.A. / Meggio, F. / Zagotto, G. / Battistutta, R. / Pinna, L.A.
History
DepositionDec 8, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)39,5622
Polymers39,2911
Non-polymers2711
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)142.410, 60.960, 45.660
Angle α, β, γ (deg.)90.000, 100.190, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-338-

HOH

-
Components

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


Mass: 39291.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: ACK2 / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli)
References: UniProt: P28523, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-CZ0 / 8-hydroxy-4-methyl-9-nitro-2H-benzo[g]chromen-2-one


Mass: 271.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H9NO5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.48 Å3/Da / Density % sol: 50.45 % / Mosaicity: 0.61 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% PEG 4000, 0.2M sodium acetate, 0.1M TrisHCl, pH 8, vapor diffusion, sitting drop, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 20, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.2→70.082 Å / Num. all: 16400 / Num. obs: 16400 / % possible obs: 83.9 % / Redundancy: 2 % / Rsym value: 0.124 / Net I/σ(I): 4.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.2-2.321.90.7930.61.1477624910.5120.7930.61.687.4
2.32-2.461.90.5850.4441.3453123330.3770.5850.4442.186.5
2.46-2.6320.5090.3851.7422021610.3290.5090.3852.585.7
2.63-2.8420.3320.2522.6394219880.2130.3320.2523.384.7
2.84-3.1120.2240.174364618200.1440.2240.174.383.9
3.11-3.4820.1430.1096.3330416280.0930.1430.1095.982.5
3.48-4.022.10.0960.0738.6293214280.0610.0960.0737.682.2
4.02-4.922.10.0860.0668.2242211740.0550.0860.0668.780.4
4.92-6.962.10.1020.0777.818719040.0660.1020.0778.478.7
6.96-41.2952.10.1180.0876.39724730.0790.1180.0879.674

-
Processing

Software
NameVersionClassificationNB
MOSFLM3.3.16data reduction
SCALA3.3.16data scaling
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: Rigid body / Resolution: 2.2→41.295 Å / Occupancy max: 1 / Occupancy min: 0.63 / FOM work R set: 0.8631 / SU ML: 0.34 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2297 847 5.17 %
Rwork0.1686 --
obs0.1718 16393 83.12 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.873 Å2 / ksol: 0.317 e/Å3
Displacement parametersBiso max: 125.68 Å2 / Biso mean: 40.0887 Å2 / Biso min: 9.89 Å2
Baniso -1Baniso -2Baniso -3
1--2.1015 Å20 Å21.7229 Å2
2--2.4354 Å20 Å2
3----0.3338 Å2
Refinement stepCycle: LAST / Resolution: 2.2→41.295 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2727 0 20 115 2862
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082818
X-RAY DIFFRACTIONf_angle_d1.1253813
X-RAY DIFFRACTIONf_chiral_restr0.082399
X-RAY DIFFRACTIONf_plane_restr0.005487
X-RAY DIFFRACTIONf_dihedral_angle_d13.9231060
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.33790.29391370.22132713285087
2.3379-2.51840.28161570.20312624278185
2.5184-2.77170.29591490.21392625277485
2.7717-3.17270.25871220.18442601272383
3.1727-3.99670.21711400.14872531267181
3.9967-41.30240.17771420.13732452259477
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)
10.376-0.39340.1780.3147-0.14090.2234-0.05310.3270.1506-0.0309-0.06230.0441-0.18070.22340.00010.2297-0.159-0.01330.25610.01090.200425.776911.1543-0.0326
20.33920.15710.35650.11290.05860.3935-0.08280.0435-0.01390.0299-0.06420.1166-0.15580.170200.2224-0.0946-0.0110.2038-0.00010.20229.065412.706614.6955
30.38270.35740.07830.3505-0.28080.525-0.0386-0.14060.02070.0326-0.01990.0032-0.150.2206-0.00010.1129-0.01330.00640.1554-0.0110.059815.08742.14412.2622
40.29940.2090.27220.29240.14530.27180.0574-0.003-0.08130.02020.019-0.15960.08010.228600.16210.06390.00280.1521-0.00760.20416.8446-14.53058.951
50.3360.2340.30710.45220.13180.29760.2571-0.1766-0.10550.3152-0.22580.02290.2511-0.02140.00230.19470.1344-0.07230.15920.04710.180313.7624-23.798610.0977
60.06350.099-0.04740.0915-0.03430.0716-0.07480.0587-0.01830.05020.1523-0.07680.0979-0.07100.14350.0145-0.01870.14270.00770.17652.2115-5.5668.5789
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN A AND RESID 7:41)A7 - 41
2X-RAY DIFFRACTION2(CHAIN A AND RESID 42:115)A42 - 115
3X-RAY DIFFRACTION3(CHAIN A AND RESID 116:193)A116 - 193
4X-RAY DIFFRACTION4(CHAIN A AND RESID 194:261)A194 - 261
5X-RAY DIFFRACTION5(CHAIN A AND RESID 262:288)A262 - 288
6X-RAY DIFFRACTION6(CHAIN A AND RESID 289:333)A289 - 333

+
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