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- PDB-4jwq: Crystal Structure of the Calcium Binding Domain of CDPK3 from Pla... -

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Basic information

Entry
Database: PDB / ID: 4jwq
TitleCrystal Structure of the Calcium Binding Domain of CDPK3 from Plasmodium Berghei, PB000947.00
ComponentsCalcium-dependent protein kinase
KeywordsTRANSFERASE / Structural Genomics / Structural Genomics Consortium / SGC / calmodulin fold
Function / homologyEF-hand / Recoverin; domain 1 / Orthogonal Bundle / Mainly Alpha / :
Function and homology information
Biological speciesPlasmodium berghei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsWernimont, A.K. / Loppnau, P. / Lin, Y.H. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Hui, R. / Mottaghi, K. / Structural Genomics Consortium (SGC)
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of the Calcium Binding Domain of CDPK3 from Plasmodium Berghei, PB000947.00
Authors: Wernimont, A.K. / Loppnau, P. / Lin, Y.H. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Hui, R. / Mottaghi, K.
History
DepositionMar 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Feb 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 / 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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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 / _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: Calcium-dependent protein kinase
C: Calcium-dependent protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3297
Polymers46,0732
Non-polymers2565
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-81 kcal/mol
Surface area8690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.564, 69.741, 90.581
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
21C

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: MET / End label comp-ID: MET / Refine code: _ / Auth seq-ID: 123 - 195 / Label seq-ID: 123 - 195

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

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Components

#1: Protein Calcium-dependent protein kinase


Mass: 23036.268 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium berghei (eukaryote) / Strain: Anka / Gene: PB000947.00.0, PBANKA_040820 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4Z443
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.35 Å3/Da / Density % sol: 47.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% Peg 4K, 0.2 M NH4SO4, 0.1 M NaCacodylate 6.5, 2 mM CaCl2, Chymotrypsin 1:100, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97934 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Mar 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 9104 / Num. obs: 9095 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rmerge(I) obs: 0.103 / Χ2: 1.727 / Net I/σ(I): 9.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.15-2.195.70.7144440.9931100
2.19-2.235.80.584521.1231100
2.23-2.275.70.5514251.1881100
2.27-2.325.90.4944401.1871100
2.32-2.375.80.4634311.2211100
2.37-2.425.70.4134551.2221100
2.42-2.485.80.3644571.1671100
2.48-2.555.80.3324391.2221100
2.55-2.625.80.2564321.381100
2.62-2.715.80.2024651.5731100
2.71-2.815.70.1944371.7061100
2.81-2.925.80.1754501.673199.8
2.92-3.055.80.1374661.741100
3.05-3.215.80.1094371.6931100
3.21-3.415.80.0894561.8811100
3.41-3.685.70.0754642.2121100
3.68-4.055.60.0654682.8081100
4.05-4.635.40.064652.5711100
4.63-5.835.50.0594822.53199.6
5.83-504.70.0585303.529199.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→38.01 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.2231 / WRfactor Rwork: 0.2007 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8267 / SU B: 10.625 / SU ML: 0.147 / SU R Cruickshank DPI: 0.2452 / SU Rfree: 0.1919 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.245 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.236 433 4.8 %RANDOM
Rwork0.2013 ---
all0.20292 9072 --
obs0.2029 9053 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 62.94 Å2 / Biso mean: 46.389 Å2 / Biso min: 11.51 Å2
Baniso -1Baniso -2Baniso -3
1--3.41 Å2-0 Å20 Å2
2--4.81 Å20 Å2
3----1.4 Å2
Refinement stepCycle: LAST / Resolution: 2.15→38.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1141 0 9 39 1189
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191167
X-RAY DIFFRACTIONr_bond_other_d0.0050.021086
X-RAY DIFFRACTIONr_angle_refined_deg1.6311.951568
X-RAY DIFFRACTIONr_angle_other_deg1.08332493
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.085140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.40525.90261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.71715217
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.034153
X-RAY DIFFRACTIONr_chiral_restr0.0850.2176
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021314
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02265
Refine LS restraints NCS

Ens-ID: 1 / Number: 3384 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2C
LS refinement shellResolution: 2.147→2.202 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 41 -
Rwork0.214 606 -
all-647 -
obs-606 98.48 %
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)
15.59783.60263.78059.3331-4.873910.2373-0.59670.39950.6072-0.5134-0.18390.1606-0.3440.73790.78060.32840.0139-0.09150.09580.05690.2754-7.007-0.3629.058
25.1752-0.95021.63742.9568-0.52174.4172-0.03980.0096-0.1654-0.0773-0.1423-0.07760.3666-0.03670.18210.18110.00060.04230.02060.04290.1617-6.846-12.07919.233
328.168-7.1438-6.267215.51676.67313.28040.19361.05520.0446-0.95950.2562-1.212-0.3746-0.0333-0.44980.25760.10330.06270.2480.0650.25083.646-14.44420.199
414.955413.7553-2.556624.80211.32341.5492-0.2261-0.4448-0.92660.50040.2238-1.4570.25670.26710.00230.30150.2206-0.14640.3322-0.00380.35426.222-16.82430.43
50.07550.0702-0.719621.1237-3.17847.1717-0.00790.0066-0.00441.0911-0.1118-0.9748-0.0541-0.05870.11960.20970.0461-0.09010.04490.05020.19371.22-10.70531.335
62.9804-7.36630.113219.54581.3271.98820.16410.06630.1871-0.2224-0.01-0.53330.20970.2365-0.15410.23050.04640.03720.1403-0.00880.1422-2.838-3.83929.342
73.4667-0.8483.71532.53190.343410.2624-0.3184-0.2828-0.06660.36590.060.2151-0.4435-0.54160.25840.21860.04920.03510.11050.02550.1004-11.261-3.40125.385
84.44732.9212.93996.618412.443525.4578-0.5870.7160.6515-0.32040.57050.2467-0.24520.71530.01650.3625-0.0619-0.16570.12250.10460.2155-5.4141.69419.493
91.00522.3701-1.36277.4356-3.13651.85120.2272-0.02530.39680.45070.30691.1194-0.29710.0536-0.53410.50510.2874-0.06830.5597-0.11660.23052.341.24425.399
105.9344-0.8054-1.54565.71012.165111.3885-0.3135-0.45380.10510.5260.213-0.14060.0713-0.25690.10050.24080.0219-0.0360.07490.01490.07294.743-2.84617.564
113.27650.27582.92432.80720.6317.61650.13810.3081-0.22340.0225-0.2091-0.17890.37190.13470.07090.178-0.00660.0190.0547-0.00290.10554.914-6.5813.777
1230.0246-3.5803-3.676424.4617-0.735521.70630.227-0.3376-1.05050.0622-0.18080.92960.8895-0.9059-0.04630.0461-0.0501-0.00980.11420.01510.0654-5.452-7.2450.703
134.30823.10077.20772.85213.8215.18970.02990.0306-0.0168-0.09010.14330.09380.1684-0.2763-0.17320.34580.0733-0.04950.2045-0.01450.0957-5.533-1.06-8.519
1426.41259.34418.48913.456910.90112.3481-0.47590.01410.8537-0.6089-0.2907-0.1613-1.1358-0.64610.76660.31840.0349-0.14930.1302-0.0610.27071.5026.644-0.735
154.8085-0.8226-0.43734.2981-0.894111.503-0.13930.40120.3971-0.019-0.2229-0.4303-0.76810.58410.36220.2366-0.0686-0.03920.07470.07840.1378.1933.164.785
162.6259-9.1112-2.286332.24948.73233.16970.1758-0.0379-0.4077-1.13970.10621.1187-0.70690.1043-0.2820.52060.08280.0510.0622-0.13790.60231.80710.80313.082
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A123 - 135
2X-RAY DIFFRACTION2A136 - 151
3X-RAY DIFFRACTION3A152 - 162
4X-RAY DIFFRACTION4A163 - 167
5X-RAY DIFFRACTION5A168 - 173
6X-RAY DIFFRACTION6A174 - 178
7X-RAY DIFFRACTION7A179 - 190
8X-RAY DIFFRACTION8A191 - 196
9X-RAY DIFFRACTION9C121 - 126
10X-RAY DIFFRACTION10C127 - 133
11X-RAY DIFFRACTION11C134 - 151
12X-RAY DIFFRACTION12C152 - 156
13X-RAY DIFFRACTION13C163 - 172
14X-RAY DIFFRACTION14C173 - 180
15X-RAY DIFFRACTION15C181 - 193
16X-RAY DIFFRACTION16C194 - 199

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