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- PDB-4o2z: Crystal Structure of MPK3 from Leishmania donovani, LdBPK_100540 ... -

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Basic information

Entry
Database: PDB / ID: 4o2z
TitleCrystal Structure of MPK3 from Leishmania donovani, LdBPK_100540 in the presence of NVP-BBT594
ComponentsMitogen-activated protein kinase 3, putative
KeywordsTRANSFERASE / neglected disease / Structural Genomics / Structural Genomics Consortium / SGC / kinase
Function / homology
Function and homology information


MAP kinase activity / mitogen-activated protein kinase / ATP binding
Similarity search - Function
Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / 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 ...Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / 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, ATP binding site / Protein kinases ATP-binding region signature. / 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-046 / Mitogen-activated protein kinase
Similarity search - Component
Biological speciesLeishmania donovani (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.71 Å
AuthorsWernimont, A.K. / Walker, J.R. / Hutchinson, A. / Loppnau, P. / Edwards, A.M. / Arrowsmith, C.H. / Bountra, C. / Hui, R. / Mangos, M. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure of MPK3 from Leishmania donovani, LdBPK_100540 in the presence of NVP-BBT594
Authors: Wernimont, A.K. / Walker, J.R. / Hutchinson, A. / Loppnau, P. / Edwards, A.M. / Arrowsmith, C.H. / Bountra, C. / Hui, R. / Mangos, M. / Structural Genomics Consortium (SGC)
History
DepositionDec 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 20, 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
A: Mitogen-activated protein kinase 3, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7902
Polymers43,2201
Non-polymers5701
Water1448
1
A: Mitogen-activated protein kinase 3, putative
hetero molecules

A: Mitogen-activated protein kinase 3, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,5804
Polymers86,4412
Non-polymers1,1392
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-x,-y,z1
Buried area1950 Å2
ΔGint-18 kcal/mol
Surface area32020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.141, 87.141, 295.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN

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Components

#1: Protein Mitogen-activated protein kinase 3, putative


Mass: 43220.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania donovani (eukaryote) / Strain: BPK282A1 / Gene: LDBPK_100540 / Plasmid: pET15-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pACYC LamP / References: UniProt: E9BA99
#2: Chemical ChemComp-046 / 5-{[6-(acetylamino)pyrimidin-4-yl]oxy}-N-{4-[(4-methylpiperazin-1-yl)methyl]-3-(trifluoromethyl)phenyl}-2,3-dihydro-1H-indole-1-carboxamide


Mass: 569.578 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H30F3N7O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 3.24 Å3/Da / Density % sol: 62.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M Citrate, 0.5 M Ammonium Sulfate, 1.0 M Lithium Sulfate, 1 mM NVP-BBT594, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.71→49.18 Å / Num. all: 16069 / Num. obs: 16037 / % possible obs: 99.8 % / Redundancy: 10.2 % / Biso Wilson estimate: 100.02 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 24.4
Reflection shell

Rmerge(I) obs: 0.015 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique all% possible all
2.71-2.8410.21.520845205299.1
8.98-49.187.972.9397050497.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO

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Processing

Software
NameVersionClassificationNB
Aimless0.2.14data scaling
PHASER2.5.5phasing
BUSTER-TNTrefinement
PDB_EXTRACT3.14data extraction
SBC-Collectdata collection
XSCALEdata scaling
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ffas03 all atom model of 3gcp

3gcp


Resolution: 2.71→48.87 Å / Cor.coef. Fo:Fc: 0.9152 / Cor.coef. Fo:Fc free: 0.9035 / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 0.515 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2664 803 5.02 %RANDOM
Rwork0.2403 ---
obs0.2416 15989 99.87 %-
all-16009 --
Displacement parametersBiso max: 215.38 Å2 / Biso mean: 103.6868 Å2 / Biso min: 71.2 Å2
Baniso -1Baniso -2Baniso -3
1--15.0933 Å20 Å20 Å2
2---15.0933 Å20 Å2
3---30.1865 Å2
Refine analyzeLuzzati coordinate error obs: 0.586 Å
Refinement stepCycle: LAST / Resolution: 2.71→48.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2813 0 41 8 2862
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d964SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes67HARMONIC2
X-RAY DIFFRACTIONt_gen_planes452HARMONIC5
X-RAY DIFFRACTIONt_it2933HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion377SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3212SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2933HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg4009HARMONIC20.88
X-RAY DIFFRACTIONt_omega_torsion1.73
X-RAY DIFFRACTIONt_other_torsion18.89
LS refinement shellResolution: 2.71→2.9 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.273 133 4.69 %
Rwork0.2672 2701 -
all0.2675 2834 -
obs--99.87 %
Refinement TLS params.Method: refined / Origin x: -10.8651 Å / Origin y: -12.5208 Å / Origin z: -23.4539 Å
111213212223313233
T-0.1245 Å20.1876 Å2-0.0819 Å2--0.0764 Å2-0.045 Å2---0.2036 Å2
L2.0496 °2-0.2943 °2-0.7017 °2-1.6619 °20.5002 °2--2.8963 °2
S-0.3797 Å °-0.1202 Å °-0.1071 Å °0.0379 Å °0.4033 Å °-0.1506 Å °-0.0854 Å °0.0351 Å °-0.0237 Å °
Refinement TLS groupSelection details: { A|* }

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