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- PDB-4ysj: Calcium-Dependent Protein Kinase from Eimeria tenella in complex ... -

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Basic information

Entry
Database: PDB / ID: 4ysj
TitleCalcium-Dependent Protein Kinase from Eimeria tenella in complex with ADP
ComponentsCalmodulin-like domain protein kinase
KeywordsTRANSFERASE / serine/threonine protein kinase / calcium-binding / ATP-binding
Function / homology
Function and homology information


protein kinase activity / phosphorylation / calcium ion binding / ATP binding
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
ADENOSINE-5'-DIPHOSPHATE / Calmodulin-like domain protein kinase
Similarity search - Component
Biological speciesEimeria tenella (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsMerritt, E.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI089441 United States
Citation
Journal: to be published
Title: CDPK is a druggable target in the apicomplexan parasite Eimeria
Authors: Ojo, K.K. / Vidadala, R. / Maly, D.J. / Van Voorhis, W.C. / Merritt, E.A.
#1: 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.M.J. / Buckner, F.S. / Parsons, M. / Hol, W.G.J. / Merritt, E.A. / Van Voorhis, W.C.
#2: Journal: ACS Med.Chem.Lett. / Year: 2014
Title: Potent and Selective Inhibitors of CDPK1 from T. gondii and C. parvum Based on a 5-Aminopyrazole-4-carboxamide Scaffold
Authors: Zhang, Z. / Ojo, K.K. / Vidadala, R. / Huang, E. / Geiger, J.A. / Scheele, S. / Choi, R. / Reid, M.C. / Keyloun, K. / Parsons, M. / Merritt, E.A. / Maly, D.J. / Verlinde, C.L.M.J. / Van Voorhis, W.C. / Fan, E.
History
DepositionMar 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Structure summary
Category: pdbx_audit_support / pdbx_struct_oper_list / struct_keywords
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.pdbx_keywords
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calmodulin-like domain protein kinase
B: Calmodulin-like domain protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,56114
Polymers111,3372
Non-polymers1,22412
Water362
1
A: Calmodulin-like domain protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2807
Polymers55,6691
Non-polymers6126
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Calmodulin-like domain protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2807
Polymers55,6691
Non-polymers6126
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.536, 108.415, 109.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 0 / Auth seq-ID: 8 - 481 / Label seq-ID: 12 - 485

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Calmodulin-like domain protein kinase


Mass: 55668.504 Da / Num. of mol.: 2 / Mutation: A410D
Source method: isolated from a genetically manipulated source
Details: cleaved N-terminal His-tag / Source: (gene. exp.) Eimeria tenella (eukaryote) / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q3HNM4
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHOR STATED THAT THE UNP REFERENCE Q3HNM4 IS INCORRECT AT RESIDUE 410. THE RESIDUE IDENTITY OF ...AUTHOR STATED THAT THE UNP REFERENCE Q3HNM4 IS INCORRECT AT RESIDUE 410. THE RESIDUE IDENTITY OF 410 SHOULD BE ASP INSTEAD OF ALA BECAUSE THIS RESIDUE IS IN BINDING TO CALCIUM AND CONSERVED ACROSS THE LARGER FAMILY OF CDPKS.

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: protein buffer: 25 mM HEPES pH 7.0, 5% glycerol, 500 mM NaCl, 2 mM DTT, 175 ??M EtCDPK1, 17.5 mM MgATP; crystallization buffer: 100 mM BIS/TRIS pH 6.5, 25% PEG 3350, 20 mM CaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.68→38.57 Å / Num. obs: 31660 / % possible obs: 99.3 % / Redundancy: 13.2 % / Biso Wilson estimate: 46.5 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.363 / Rpim(I) all: 0.103 / Net I/σ(I): 6.6 / Num. measured all: 417423 / Scaling rejects: 123
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.68-2.8211.43.4510.94554639810.5181.04895.2
8.91-38.5711.80.06519.6115409740.9990.0298.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.25 Å38.57 Å
Translation6.25 Å38.57 Å

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
PHASER2.5.6phasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→38.57 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.898 / WRfactor Rfree: 0.2703 / WRfactor Rwork: 0.2249 / FOM work R set: 0.6623 / SU B: 45.303 / SU ML: 0.409 / SU R Cruickshank DPI: 0.3367 / SU Rfree: 0.4017 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.402 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2917 1522 4.9 %RANDOM
Rwork0.2464 ---
obs0.2486 29593 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 151.88 Å2 / Biso mean: 78.058 Å2 / Biso min: 28.54 Å2
Baniso -1Baniso -2Baniso -3
1-2.08 Å2-0 Å20 Å2
2--3.75 Å20 Å2
3----5.83 Å2
Refinement stepCycle: final / Resolution: 2.7→38.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7343 0 64 2 7409
Biso mean--50.55 40.75 -
Num. residues----921
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0197583
X-RAY DIFFRACTIONr_bond_other_d0.0040.027249
X-RAY DIFFRACTIONr_angle_refined_deg1.5631.9810133
X-RAY DIFFRACTIONr_angle_other_deg0.955316719
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8075915
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.8424.77348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.342151414
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2531540
X-RAY DIFFRACTIONr_chiral_restr0.0760.21131
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028345
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021657
X-RAY DIFFRACTIONr_mcbond_it1.9933.3383685
X-RAY DIFFRACTIONr_mcbond_other1.9923.3383684
X-RAY DIFFRACTIONr_mcangle_it3.2565.0054587
Refine LS restraints NCS

Ens-ID: 1 / Number: 29065 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.432 117 -
Rwork0.399 2024 -
all-2141 -
obs--93.94 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.25690.79791.62543.8862.17571.95280.0455-0.24170.05840.27-0.22110.2826-0.0047-0.22850.17560.3479-0.01680.03670.0637-0.07490.842641.74557.475142.761
22.42890.20722.04871.95711.38692.61220.10960.13730.0461-0.2057-0.17210.0043-0.17440.04990.06250.2887-0.0380.06770.0465-0.03430.920537.0155.838129.122
35.1404-1.074-0.32092.84741.16573.74070.21560.3550.1083-0.0565-0.27570.1816-0.0706-0.19540.06010.19170.0226-0.00310.0499-0.08450.821721.97754.947119.288
41.87840.40020.57143.25661.07243.15440.10130.0216-0.0461-0.0845-0.0662-0.09660.07350.1308-0.03510.2954-0.04040.02050.01990.0410.873249.62436.477134.803
51.75040.0723.7331.2294-0.991119.2861-0.00370.0042-0.6450.3419-0.5587-0.09671.41591.86230.56240.94560.2787-0.00310.60460.20741.309460.70335.348152.753
62.8092-0.47291.25725.21190.14413.3352-0.0041-0.2430.11590.21340.0370.2082-0.2616-0.1675-0.03290.2452-0.04460.02170.0393-0.06930.789642.87498.48989.733
71.9038-0.12591.69271.53391.19933.5330.1642-0.11640.044-0.0127-0.19130.1154-0.0417-0.0310.02710.2837-0.05780.06270.0975-0.05240.91434.73294.10475.963
83.2368-0.4336-0.29023.12340.59463.93160.1680.35140.0883-0.1762-0.31190.1358-0.0232-0.22160.14390.18960.00580.01260.0707-0.0350.769223.52393.83762.453
92.53370.56681.23274.36512.42382.63990.0980.3062-0.05-0.6033-0.0091-0.09730.04690.3228-0.08890.48820.0359-0.01980.09860.02040.914249.03673.80974.227
105.11710.8605-2.33653.0875-0.43897.9082-0.0251-0.6029-0.27350.3216-0.1235-0.29480.45780.60770.14860.5426-0.0496-0.0740.18630.09350.896356.00478.28996.777
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 89
2X-RAY DIFFRACTION2A90 - 179
3X-RAY DIFFRACTION3A180 - 285
4X-RAY DIFFRACTION4A286 - 456
5X-RAY DIFFRACTION4A501
6X-RAY DIFFRACTION4A502
7X-RAY DIFFRACTION4A503
8X-RAY DIFFRACTION5A457 - 481
9X-RAY DIFFRACTION5A504
10X-RAY DIFFRACTION6B8 - 78
11X-RAY DIFFRACTION7B79 - 194
12X-RAY DIFFRACTION8B195 - 290
13X-RAY DIFFRACTION9B293 - 409
14X-RAY DIFFRACTION9B501
15X-RAY DIFFRACTION9B502
16X-RAY DIFFRACTION10B410 - 481
17X-RAY DIFFRACTION10B503
18X-RAY DIFFRACTION10B504

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