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- PDB-2pmo: Crystal structure of PfPK7 in complex with hymenialdisine -

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Basic information

Entry
Database: PDB / ID: 2pmo
TitleCrystal structure of PfPK7 in complex with hymenialdisine
ComponentsSer/Thr 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
Chem-HMD / mitogen-activated protein kinase kinase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsMerckx, A. / Echalier, A. / Noble, M. / Endicott, J.
CitationJournal: Structure / Year: 2008
Title: Structures of P. falciparum protein kinase 7 identify an 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 1.2Aug 30, 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 / 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_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

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Assembly

Deposited unit
X: Ser/Thr protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7592
Polymers41,4351
Non-polymers3241
Water64936
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.061, 82.473, 138.717
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11X-425-

HOH

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Components

#1: Protein Ser/Thr protein kinase


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
#2: Chemical ChemComp-HMD / 4-(5-AMINO-4-OXO-4H-PYRAZOL-3-YL)-2-BROMO-4,5,6,7-TETRAHYDRO-3AH-PYRROLO[2,3-C]AZEPIN-8-ONE / HYMENIALDISINE


Mass: 324.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H10BrN5O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.52 Å3/Da / Density % sol: 51.21 %
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: ID14-3 / Wavelength: 0.931 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 10, 2005
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.9→69.34 Å / Num. obs: 9580 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 11
Reflection shellResolution: 2.9→2.975 Å / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 2.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DNAdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PfPK7 in complex with an ATP analogue (2PML)

2pml


Resolution: 2.9→69.34 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.849 / SU B: 43.103 / SU ML: 0.427 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.529 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.3158 460 4.8 %RANDOM
Rwork0.23044 ---
obs0.23453 9098 99.5 %-
all-9580 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.177 Å2
Baniso -1Baniso -2Baniso -3
1-3.82 Å20 Å20 Å2
2---1.77 Å20 Å2
3----2.05 Å2
Refinement stepCycle: LAST / Resolution: 2.9→69.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2856 0 19 36 2911
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222951
X-RAY DIFFRACTIONr_angle_refined_deg1.3751.9793970
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0185340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.00224.83147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.84615575
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.831512
X-RAY DIFFRACTIONr_chiral_restr0.090.2422
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022204
X-RAY DIFFRACTIONr_nbd_refined0.2120.21346
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21973
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.296
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2860.23
X-RAY DIFFRACTIONr_mcbond_it0.3271.51752
X-RAY DIFFRACTIONr_mcangle_it0.58122775
X-RAY DIFFRACTIONr_scbond_it0.57431369
X-RAY DIFFRACTIONr_scangle_it0.8424.51195
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.497 20 -
Rwork0.301 653 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -11.64 Å / Origin y: -24.8097 Å / Origin z: -20.308 Å
111213212223313233
T0.0009 Å20.006 Å20.0714 Å2-0.0263 Å2-0.0145 Å2---0.0897 Å2
L3.2477 °2-0.4942 °20.7885 °2-4.0875 °2-1.0845 °2--3.2155 °2
S0.1131 Å °0.29 Å °0.2731 Å °-0.3981 Å °-0.0595 Å °0.1762 Å °-0.2394 Å °-0.0466 Å °-0.0536 Å °

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