[English] 日本語
Yorodumi
- PDB-3i79: Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3i79
TitleCalcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1)
ComponentsCalmodulin-domain protein kinase 1
KeywordsTRANSFERASE / protein kinase / calmodulin / EF hand / bumped kinase inhibitor / ATP-binding / Kinase / Nucleotide-binding / Serine/threonine-protein kinase / Structural Genomics / Medical Structural Genomics of Pathogenic Protozoa / MSGPP
Function / homology
Function and homology information


phosphorylation / protein serine/threonine kinase activity / calcium ion binding / ATP binding / membrane / cytoplasm
Similarity search - Function
EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 ...EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / 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
Calmodulin-domain protein kinase 1
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.04 Å
AuthorsLarson, E.T. / Merritt, E.A. / Medical Structural Genomics of Pathogenic Protozoa (MSGPP)
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Toxoplasma gondii calcium-dependent protein kinase 1 is a target for selective kinase inhibitors.
Authors: Ojo, K.K. / Larson, E.T. / Keyloun, K.R. / Castaneda, L.J. / Derocher, A.E. / Inampudi, K.K. / Kim, J.E. / Arakaki, T.L. / Murphy, R.C. / Zhang, L. / Napuli, A.J. / Maly, D.J. / Verlinde, C. ...Authors: Ojo, K.K. / Larson, E.T. / Keyloun, K.R. / Castaneda, L.J. / Derocher, A.E. / Inampudi, K.K. / Kim, J.E. / Arakaki, T.L. / Murphy, R.C. / Zhang, L. / Napuli, A.J. / Maly, D.J. / Verlinde, C.L. / Buckner, F.S. / Parsons, M. / Hol, W.G. / Merritt, E.A. / Van Voorhis, W.C.
#1: Journal: ACS Med Chem Lett / Year: 2010
Title: Discovery of Potent and Selective Inhibitors of Calcium-Dependent Protein Kinase 1 (CDPK1) from C. parvum and T. gondii.
Authors: Murphy, R.C. / Ojo, K.K. / Larson, E.T. / Castellanos-Gonzalez, A. / Perera, B.G. / Keyloun, K.R. / Kim, J.E. / Bhandari, J.G. / Muller, N.R. / Verlinde, C.L. / White, A.C. / Merritt, E.A. / ...Authors: Murphy, R.C. / Ojo, K.K. / Larson, E.T. / Castellanos-Gonzalez, A. / Perera, B.G. / Keyloun, K.R. / Kim, J.E. / Bhandari, J.G. / Muller, N.R. / Verlinde, C.L. / White, A.C. / Merritt, E.A. / Van Voorhis, W.C. / Maly, D.J.
History
DepositionJul 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 12, 2014Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Feb 21, 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: Calmodulin-domain protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2892
Polymers55,2271
Non-polymers621
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.144, 71.861, 67.265
Angle α, β, γ (deg.)90.00, 102.98, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Calmodulin-domain protein kinase 1


Mass: 55226.914 Da / Num. of mol.: 1 / Fragment: residues 30-507
Source method: isolated from a genetically manipulated source
Details: residues 1-29 were replaced with a 3C cleavable His-tag and linker during cloning; tag was cleaved prior to crystallization
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: CDPK1 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9BJF5, Ca2+/calmodulin-dependent protein kinase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.05 Å3/Da / Density % sol: 40.09 %
Crystal growTemperature: 298 K / Method: sitting drop vapor diffusion / pH: 6.5
Details: 25% PEG 3350, 0.2 M tri-ammonium citrate; cryoprotected with 15% ethylene glycol, pH 6.5, sitting drop vapor diffusion, temperature 298K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL9-210.97923
SYNCHROTRONSSRL BL9-220.97923
Detector
TypeIDDetectorDate
MarUSA MarMosaic -325 CCD1CCDApr 22, 2009
MarUSA MarMosaic -325 CCD2CCDApr 22, 2009
Radiation
IDMonochromatorProtocolScattering typeWavelength-ID
1Double crystalSADx-ray1
2Double crystalSINGLE WAVELENGTHx-ray1
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionRedundancy: 7.7 % / Av σ(I) over netI: 27.54 / Number: 154144 / Rmerge(I) obs: 0.109 / Χ2: 1.03 / D res high: 2.3 Å / D res low: 50 Å / Num. obs: 20099 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.955099.810.051.0097.5
3.934.9510010.0491.1077.7
3.443.9310010.0741.0887.7
3.123.4410010.1131.0827.7
2.93.1210010.1831.067.7
2.732.910010.31.047.7
2.592.7310010.4510.9877.7
2.482.5910010.6470.9827.7
2.382.4810010.7850.9717.7
2.32.3810010.9540.9697.7
ReflectionResolution: 2.04→50 Å / Num. obs: 28324 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 4.2 % / Biso Wilson estimate: 34.8 Å2 / Rmerge(I) obs: 0.052 / Χ2: 1.04 / Net I/σ(I): 10.4
Reflection shellResolution: 2.04→2.12 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2799 / Χ2: 1.041 / % possible all: 100

-
Phasing

PhasingMethod: SAD
Phasing MADD res high: 2.68 Å / D res low: 50 Å / FOM : 0.34 / Reflection: 12526
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se600.9510.4630.1890.501
2Se43.8290.6720.6490.1140.745
3Se45.1570.20.050.0690.635
4Se41.7470.090.0920.1740.588
5Se600.9880.4610.4120.571
6Se52.2920.6870.730.3650.534
7Se24.0010.4150.6410.0630.281
8Se600.4290.0050.1430.49
9Se600.1070.8120.2060.458
10Se600.8890.3460.2370.486
11Se600.8170.3830.2310.399
12Se31.9090.0110.7980.4280.221
Phasing MAD shell
Resolution (Å)FOM Reflection
9.68-500.47597
6.1-9.680.481046
4.77-6.10.471327
4.04-4.770.441558
3.57-4.040.371778
3.23-3.570.311937
2.97-3.230.252069
2.77-2.970.182214
Phasing dmFOM : 0.65 / FOM acentric: 0.64 / FOM centric: 0.67 / Reflection: 19305 / Reflection acentric: 18508 / Reflection centric: 797
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6.6-39.3240.920.930.86887775112
4.1-6.60.890.90.8426842513171
3.3-4.10.810.820.7233453196149
2.9-3.30.630.630.5633093189120
2.5-2.90.510.510.4857005534166
2.3-2.50.460.460.453380330179

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.13phasing
RESOLVE2.13phasing
REFMACrefmac_5.5.0096refinement
PDB_EXTRACT3.005data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.04→36.89 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.262 / WRfactor Rwork: 0.211 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 12.26 / SU ML: 0.152 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.249 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES ARE RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1431 5.1 %RANDOM
Rwork0.213 ---
obs0.215 28302 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 61.65 Å2 / Biso mean: 30.032 Å2 / Biso min: 6.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20.89 Å2
2---0.7 Å20 Å2
3---0.97 Å2
Refinement stepCycle: LAST / Resolution: 2.04→36.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3650 0 4 75 3729
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223739
X-RAY DIFFRACTIONr_bond_other_d0.0010.022609
X-RAY DIFFRACTIONr_angle_refined_deg0.8661.9715026
X-RAY DIFFRACTIONr_angle_other_deg0.76936384
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.665461
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.31424.944178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.15715734
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5221521
X-RAY DIFFRACTIONr_chiral_restr0.050.2558
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024108
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02733
X-RAY DIFFRACTIONr_mcbond_it1.17742268
X-RAY DIFFRACTIONr_mcbond_other0.2654932
X-RAY DIFFRACTIONr_mcangle_it2.02563661
X-RAY DIFFRACTIONr_scbond_it2.14361471
X-RAY DIFFRACTIONr_scangle_it3.471101361
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.044-2.0970.2851120.2661910210396.148
2.097-2.1540.283920.24219242016100
2.154-2.2170.282880.2311889197899.949
2.217-2.2850.2731020.2341826192999.948
2.285-2.360.27740.21517621836100
2.36-2.4430.2561020.20817191821100
2.443-2.5350.275990.21316681767100
2.535-2.6380.225860.2415791665100
2.638-2.7550.264690.23315301599100
2.755-2.8890.299760.22414691545100
2.889-3.0450.229730.2251387146199.932
3.045-3.2290.272700.23513331403100
3.229-3.4520.268650.21912341299100
3.452-3.7280.273650.21911521217100
3.728-4.0820.246610.18510641125100
4.082-4.5620.189620.182951101699.705
4.562-5.2630.239440.19857901100
5.263-6.4360.361530.235710763100
6.436-9.0580.172190.19158560599.835
9.058-65.5120.281190.17832235097.429
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)
14.5352-2.53381.51745.0096-1.32324.8438-0.15790.02130.31630.15540.046-0.1739-0.5108-0.02270.11190.2352-0.0275-0.07890.1485-0.00930.200613.47217.44472.971
20.7495-0.47680.29791.917-0.66632.99990.0297-0.02320.06250.0406-0.1114-0.13340.12190.18540.08170.1687-0.0139-0.01880.2119-0.02140.218410.11514.92258.175
32.2812-0.3340.23323.61150.52592.18510.09030.25520.0585-0.5442-0.1442-0.04820.08870.16280.05390.240.0503-0.02020.2213-0.01180.12216.62822.52241.035
41.1013-0.0988-0.02592.47112.90428.6606-0.11180.0979-0.00070.63490.2199-0.37140.76070.2137-0.10820.29980.0751-0.0420.18020.0170.343925.35628.86368.062
54.4142-8.4739-2.378219.5609-1.177411.31140.14610.51420.5457-0.1894-0.7557-1.51580.1779-0.54340.60960.33180.0788-0.32850.2258-0.02130.566828.57226.11579.59
68.6664-2.8575-3.39420.99171.35925.69310.15210.29020.1846-0.02120.0162-0.0208-0.3597-0.0443-0.16830.16740.05310.0150.24160.090.308931.04839.65753.458
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A45 - 93
2X-RAY DIFFRACTION2A94 - 213
3X-RAY DIFFRACTION3A214 - 314
4X-RAY DIFFRACTION4A315 - 387
5X-RAY DIFFRACTION5A388 - 442
6X-RAY DIFFRACTION6A443 - 507

+
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