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- PDB-2pml: Crystal structure of PfPK7 in complex with an ATP analogue -

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Basic information

Entry
Database: PDB / ID: 2pml
TitleCrystal structure of PfPK7 in complex with an ATP analogue
ComponentsSer/Thr protein kinaseSerine/threonine-specific protein kinase
KeywordsTRANSFERASE / Ser/Thr protein kinase / Plasmodium falciparum / phosphorylation
Function / homology
Function and homology information


JUN kinase kinase activity / mitotic DNA damage checkpoint signaling / mitogen-activated protein kinase kinase / MAP kinase kinase activity / protein kinase activity / phosphorylation / protein serine/threonine kinase activity / ATP binding / nucleus / cytoplasm
Similarity search - Function
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 domain profile. / Protein kinase domain ...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 domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / : / Protein kinase domain-containing protein / mitogen-activated protein kinase kinase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsMerckx, A. / Echalier, A. / Noble, M. / Endicott, J.
CitationJournal: To be Published
Title: Structures of PfPK7 an atypical protein kinase from P. falciparum identify a novel activation motif and leads for inhibitor design
Authors: Merckx, A. / Echalier, A. / Langford, K. / Sicard, A. / Langsley, G. / Joore, J. / Doerig, C. / Noble, M. / Endicott, J.
History
DepositionApr 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). Authors ... THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). Authors state that the biological unit is unknown.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Ser/Thr protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9963
Polymers41,4351
Non-polymers5612
Water48627
1
X: Ser/Thr protein kinase
hetero molecules

X: Ser/Thr protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,9916
Polymers82,8692
Non-polymers1,1224
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area4690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.554, 81.795, 138.273
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN

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Components

#1: Protein Ser/Thr protein kinase / Serine/threonine-specific protein kinase / PfPK7


Mass: 41434.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PFB0605w / Plasmid: pGEX / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q7YTF7, UniProt: O96214*PLUS
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.47 Å3/Da / Density % sol: 50.3 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Hepes pH7.5; 20% PEG 10K, VAPOR DIFFUSION, SITTING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9762, 0.9791, 0.9792, 0.9686
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 10, 2005
RadiationMonochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97621
20.97911
30.97921
40.96861
ReflectionResolution: 2.6→20 Å / Num. obs: 13019 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 24.1
Reflection shellResolution: 2.6→2.666 Å / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 4.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DNAdata collection
MOSFLMdata reduction
SCALAdata scaling
SHELXSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.884 / SU B: 30.868 / SU ML: 0.346 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 1.477 / ESU R Free: 0.421 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.32705 629 4.9 %RANDOM
Rwork0.2576 ---
obs0.261 12330 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.535 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20 Å2
2--0.14 Å20 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2856 0 32 27 2915
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222963
X-RAY DIFFRACTIONr_angle_refined_deg1.3491.9843991
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4845340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.60124.83147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.82415575
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5011512
X-RAY DIFFRACTIONr_chiral_restr0.1030.2426
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022190
X-RAY DIFFRACTIONr_nbd_refined0.2240.21445
X-RAY DIFFRACTIONr_nbtor_refined0.3130.22019
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2101
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2570.25
X-RAY DIFFRACTIONr_mcbond_it0.4781.51759
X-RAY DIFFRACTIONr_mcangle_it0.81322775
X-RAY DIFFRACTIONr_scbond_it0.93131385
X-RAY DIFFRACTIONr_scangle_it1.474.51216
LS refinement shellResolution: 2.6→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 55 -
Rwork0.334 862 -
obs--99.89 %
Refinement TLS params.Method: refined / Origin x: -12.052 Å / Origin y: 16.63 Å / Origin z: -20.748 Å
111213212223313233
T0.1332 Å2-0.0404 Å20.0855 Å2--0.0963 Å2-0.0102 Å2---0.284 Å2
L3.6646 °2-0.188 °20.4667 °2-4.3743 °2-1.2475 °2--3.2981 °2
S0.1714 Å °0.3739 Å °0.2149 Å °-0.4295 Å °-0.0846 Å °0.1516 Å °0.1407 Å °0.0859 Å °-0.0868 Å °

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