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- PDB-3q5i: Crystal Structure of PBANKA_031420 -

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Basic information

Entry
Database: PDB / ID: 3q5i
TitleCrystal Structure of PBANKA_031420
ComponentsProtein kinase
KeywordsTRANSFERASE / CDPK / plasmodium / malaria / calcium dependent protein kinase / phosphotransferase / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / :
Similarity search - Component
Biological speciesPlasmodium berghei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsWernimont, A.K. / Hutchinson, A. / Sullivan, H. / Panico, E. / Crombet, L. / Cossar, D. / Hassani, A. / Vedadi, M. / Arrowsmith, C.H. / Edwards, A.M. ...Wernimont, A.K. / Hutchinson, A. / Sullivan, H. / Panico, E. / Crombet, L. / Cossar, D. / Hassani, A. / Vedadi, M. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Hui, R. / Neculai, A.M. / Amani, M. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure of CDPK1 from Plasmodium Bergheii, PBANKA_031420
Authors: Wernimont, A.K. / Hutchinson, A. / Sullivan, H. / Panico, E. / Crombet, L. / Cossar, D. / Hassani, A. / Vedadi, M. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Hui, R. / ...Authors: Wernimont, A.K. / Hutchinson, A. / Sullivan, H. / Panico, E. / Crombet, L. / Cossar, D. / Hassani, A. / Vedadi, M. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Hui, R. / Neculai, A.M. / Amani, M.
History
DepositionDec 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version
Revision 1.4Sep 13, 2023Group: 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_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7399
Polymers58,9681
Non-polymers7718
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.467, 107.138, 54.303
Angle α, β, γ (deg.)90.00, 108.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein kinase /


Mass: 58968.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium berghei (eukaryote) / Strain: ANKA / Gene: PB000158.03.0, PBANKA_031420 / Plasmid: PET15mlh / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q4YRR5
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O

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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: 2.27 Å3/Da / Density % sol: 45.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20 % PEG 3350, 0.2 M CaCl2, 5 mM AMPPNP, 5 mM CaCL2, 2.5 mM MgCl2, glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Sep 21, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.1→53.57 Å / Num. all: 30757 / Num. obs: 30757 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 7.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.1-2.144.20.9161.72199.9
2.14-2.184.20.8261.951100
2.18-2.224.20.7142.31100
2.22-2.264.20.618199.9
2.26-2.314.20.5851100
2.31-2.374.30.4791100
2.37-2.424.30.451100
2.42-2.494.30.4031100
2.49-2.564.30.3481100
2.56-2.654.30.3061100
2.65-2.744.30.2551100
2.74-2.854.30.2051100
2.85-2.984.30.1641100
2.98-3.144.30.1221100
3.14-3.334.30.0881100
3.33-3.594.30.0721100
3.59-3.954.30.0671100
3.95-4.524.30.0471100
4.52-5.74.30.0371100
5.7-504.20.029199.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 53.39 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å46.47 Å
Translation2.5 Å46.47 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
SCALEPACKdata scaling
PHASER2.1.4phasing
TNTrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3hx4

3hx4


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.907 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 10.606 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.23 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25025 1545 5 %RANDOM
Rwork0.19443 ---
obs0.19723 29135 99.72 %-
all-30757 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.752 Å2
Baniso -1Baniso -2Baniso -3
1-1.17 Å20 Å20.08 Å2
2---0.5 Å20 Å2
3----0.62 Å2
Refine analyzeLuzzati coordinate error obs: 0.272 Å
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3707 0 38 222 3967
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223861
X-RAY DIFFRACTIONr_bond_other_d0.0010.022593
X-RAY DIFFRACTIONr_angle_refined_deg1.5141.9675214
X-RAY DIFFRACTIONr_angle_other_deg1.22336336
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6915478
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.93225.135185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.49415689
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0861515
X-RAY DIFFRACTIONr_chiral_restr0.1020.2570
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024316
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02790
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2051.52355
X-RAY DIFFRACTIONr_mcbond_other0.1391.5972
X-RAY DIFFRACTIONr_mcangle_it2.19323763
X-RAY DIFFRACTIONr_scbond_it3.06531506
X-RAY DIFFRACTIONr_scangle_it5.2044.51448
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 108 -
Rwork0.301 2114 -
obs--98.41 %
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)
10.7171-0.5294-1.03191.20380.86311.5980.13980.08320.0180.1217-0.05960.0982-0.0247-0.1739-0.08030.2849-0.0116-0.01230.2907-0.01240.2917-12.1109-13.9389-11.6306
20.2598-0.3778-0.40521.3408-0.28171.68440.13580.02490.0181-0.232-0.06060.0132-0.014-0.0241-0.07520.32670.0499-0.01310.2970.00030.2656-3.8011-14.8823-30.7292
31.3516-0.7925-0.89640.9680.53720.9835-0.08110.0598-0.0560.0572-0.00210.02670.201-0.09110.08320.3187-0.0169-0.00140.2851-0.0080.2618-0.1219-33.8875-34.6015
40.1321-0.073-0.41160.32470.58061.9669-0.0295-0.12950.00030.150.13910.03910.10450.4235-0.10960.32840.0538-0.01940.3586-0.00610.24597.8646-18.0839-10.2612
50.9864-0.9570.03710.9779-0.24941.2386-0.0883-0.1970.02860.0180.1768-0.04920.21820.1945-0.08850.30540.0637-0.06240.341-0.00430.25696.1013-21.7294-3.4272
65.7596-0.0120.16910.0397-0.02783.1315-0.21290.43842.00270.0980.05830.0906-1.2719-0.29270.15460.87250.1865-0.07070.31560.25821.1124-5.55450.6862-9.9614
70.8869-0.4996-0.53460.61150.43311.40080.08470.0169-0.07630.1163-0.02530.1327-0.0259-0.1264-0.05940.3527-0.00390.04440.25290.03890.3098-15.065-5.43721.2989
82.5757-0.8419-0.0185.1958-0.41960.121-0.1605-0.13310.43460.69790.1882-0.8904-0.1523-0.1521-0.02770.44610.1273-0.00910.2874-0.00690.473-4.70352.0045-0.7996
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 55
2X-RAY DIFFRACTION2A56 - 182
3X-RAY DIFFRACTION3A183 - 330
4X-RAY DIFFRACTION4A331 - 404
5X-RAY DIFFRACTION5A405 - 446
6X-RAY DIFFRACTION6A447 - 472
7X-RAY DIFFRACTION7A473 - 502
8X-RAY DIFFRACTION8A503 - 518

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