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- PDB-4yga: CDPK1, from Toxoplasma gondii, bound to inhibitory VHH-1B7 -

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Basic information

Entry
Database: PDB / ID: 4yga
TitleCDPK1, from Toxoplasma gondii, bound to inhibitory VHH-1B7
Components
  • Calmodulin-domain protein kinase 1
  • VHH-1B7
KeywordsMETAL BINDING PROTEIN / Serine/Threonine Protein Kinase / VHH Domain / Inhibitor
Function / homology
Function and homology information


protein serine/threonine kinase activity / calcium ion binding / ATP binding / membrane
Similarity search - Function
: / EF-hand / Recoverin; 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 ...: / EF-hand / Recoverin; 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 / Immunoglobulins / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Calmodulin-domain protein kinase 1
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.94 Å
AuthorsKnockenhauer, K.E. / Schwartz, T.U.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Office of the Director1DP5OD017892 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Allosteric activation of apicomplexan calcium-dependent protein kinases.
Authors: Ingram, J.R. / Knockenhauer, K.E. / Markus, B.M. / Mandelbaum, J. / Ramek, A. / Shan, Y. / Shaw, D.E. / Schwartz, T.U. / Ploegh, H.L. / Lourido, S.
History
DepositionFeb 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Database references
Revision 1.2Sep 23, 2015Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calmodulin-domain protein kinase 1
B: VHH-1B7
C: Calmodulin-domain protein kinase 1
D: VHH-1B7
E: Calmodulin-domain protein kinase 1
F: VHH-1B7
G: Calmodulin-domain protein kinase 1
H: VHH-1B7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)296,55224
Polymers295,9108
Non-polymers64116
Water00
1
A: Calmodulin-domain protein kinase 1
B: VHH-1B7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,1386
Polymers73,9782
Non-polymers1604
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Calmodulin-domain protein kinase 1
D: VHH-1B7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,1386
Polymers73,9782
Non-polymers1604
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Calmodulin-domain protein kinase 1
F: VHH-1B7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,1386
Polymers73,9782
Non-polymers1604
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Calmodulin-domain protein kinase 1
H: VHH-1B7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,1386
Polymers73,9782
Non-polymers1604
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.920, 91.067, 106.641
Angle α, β, γ (deg.)88.71, 108.27, 90.26
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Calmodulin-domain protein kinase 1


Mass: 58535.398 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: CDPK1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)V2RpAcYc-LIC+LamP / References: UniProt: Q9BJF5
#2: Antibody
VHH-1B7


Mass: 15442.187 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-LOBSTR-RIL
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ca
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% w/v PEG 3350, 0.2 M ammonium sulfate, 0.1 M Bis-Tris pH 6.5, 4% v/v 1-propanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.94→73.04 Å / Num. obs: 53985 / % possible obs: 93.5 % / Redundancy: 3.9 % / Rsym value: 0.11 / Net I/σ(I): 10.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.94→70.67 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.93 / Phase error: 33.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2619 1715 3.18 %
Rwork0.2258 --
obs0.227 53942 92.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.94→70.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17332 0 16 0 17348
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00317635
X-RAY DIFFRACTIONf_angle_d0.77523853
X-RAY DIFFRACTIONf_dihedral_angle_d12.636231
X-RAY DIFFRACTIONf_chiral_restr0.032735
X-RAY DIFFRACTIONf_plane_restr0.0033069
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.94-3.02650.34831400.31933822X-RAY DIFFRACTION81
3.0265-3.12420.33551350.30744421X-RAY DIFFRACTION94
3.1242-3.23590.32851470.29584449X-RAY DIFFRACTION94
3.2359-3.36540.32451410.28324245X-RAY DIFFRACTION90
3.3654-3.51860.31671430.27194500X-RAY DIFFRACTION95
3.5186-3.70410.30191540.25994459X-RAY DIFFRACTION95
3.7041-3.93620.30911510.23034431X-RAY DIFFRACTION93
3.9362-4.240.21471330.1984302X-RAY DIFFRACTION91
4.24-4.66670.20791480.18494459X-RAY DIFFRACTION95
4.6667-5.34170.26721360.19794402X-RAY DIFFRACTION93
5.3417-6.72920.29711360.24944393X-RAY DIFFRACTION93
6.7292-70.69060.22151510.20244344X-RAY DIFFRACTION92

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