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- PDB-3uib: Map kinase LMAMPK10 from leishmania major in complex with SB203580 -

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Basic information

Entry
Database: PDB / ID: 3uib
TitleMap kinase LMAMPK10 from leishmania major in complex with SB203580
Componentsmitogen-activated protein kinase
KeywordsTRANSFERASE / eukariotic PROTEIN KINASE FOLD
Function / homology
Function and homology information


MAP kinase activity / intracellular signal transduction / phosphorylation / ATP binding / nucleus / cytoplasm
Similarity search - Function
Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle ...Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase 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-SB2 / Putative mitogen-activated protein kinase
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / molecular replacement / Resolution: 2.65 Å
AuthorsHorjales, S. / Schmidt-Arras, D. / Leclercq, O. / Spath, G. / Buschiazzo, A.
CitationJournal: Structure / Year: 2012
Title: The Crystal Structure of the MAP Kinase LmaMPK10 from Leishmania Major Reveals Parasite-Specific Features and Regulatory Mechanisms.
Authors: Horjales, S. / Schmidt-Arras, D. / Limardo, R.R. / Leclercq, O. / Obal, G. / Prina, E. / Turjanski, A.G. / Spath, G.F. / Buschiazzo, A.
History
DepositionNov 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: mitogen-activated protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8372
Polymers41,4591
Non-polymers3771
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.900, 80.900, 131.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein mitogen-activated protein kinase


Mass: 41459.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: LMJF10.0200, LMJF_10_0200 / Plasmid: PQE80 / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 F
References: UniProt: Q4QHJ8, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-SB2 / 4-[5-(4-FLUORO-PHENYL)-2-(4-METHANESULFINYL-PHENYL)-3H-IMIDAZOL-4-YL]-PYRIDINE


Mass: 377.435 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H16FN3OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.59 Å3/Da / Density % sol: 52.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 12% PEG 4000, 0.1M HEPES, 4% ISOPROPANOL, 5% GLYCEROL,(ligand SB203580 was introduced by soaking), pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 20, 2010
RadiationMonochromator: VARIMAX-HF MULTILAYER MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.65→43.09 Å / Num. all: 13224 / Num. obs: 13224 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 64.75 Å2 / Rsym value: 0.09 / Net I/σ(I): 13.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.63-2.774.50.5871.30.587184.3
2.77-2.944.60.6011.30.6011100
2.94-3.154.60.38120.3811100
3.15-3.44.60.2163.60.2161100
3.4-3.724.60.1266.10.1261100
3.72-4.164.60.07110.60.0711100
4.16-4.814.50.04615.50.0461100
4.81-5.894.50.053130.0531100
5.89-8.324.30.02825.30.0281100
8.32-43.08940.01637.90.016198.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.15data scaling
AMoREphasing
BUSTER-TNTrefinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
MOSFLMdata reduction
BUSTER2.10.0refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.65→43.09 Å / Cor.coef. Fo:Fc: 0.9155 / Cor.coef. Fo:Fc free: 0.9064 / Occupancy max: 1 / Occupancy min: 0.47 / SU R Cruickshank DPI: 0.486 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: TLS model (two groups)
RfactorNum. reflection% reflectionSelection details
Rfree0.2411 997 7.56 %RANDOM
Rwork0.2152 ---
obs0.2171 13181 99.47 %-
all-13181 --
Displacement parametersBiso mean: 76.15 Å2
Baniso -1Baniso -2Baniso -3
1--2.3821 Å20 Å20 Å2
2---2.3821 Å20 Å2
3---4.7642 Å2
Refine analyzeLuzzati coordinate error obs: 0.386 Å
Refinement stepCycle: LAST / Resolution: 2.65→43.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2422 0 27 59 2508
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082504HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.043402HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d829SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes56HARMONIC2
X-RAY DIFFRACTIONt_gen_planes387HARMONIC5
X-RAY DIFFRACTIONt_it2504HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.25
X-RAY DIFFRACTIONt_other_torsion20.67
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion331SEMIHARMONIC5
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_contact2831SEMIHARMONIC4
LS refinement shellResolution: 2.65→2.86 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2557 206 7.87 %
Rwork0.2353 2413 -
all0.2369 2619 -
obs--99.47 %
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)
13.167-0.21092.91040.7084-0.16110.05890.0382-0.09310.02740.1868-0.0602-0.37980.11920.29950.022-0.25220.10620.02140.29910.0588-0.02049.748519.963743.1677
21.9330.3563-0.82972.62020.60613.71520.117-0.26080.4141-0.133-0.0666-0.1498-0.53940.2235-0.0504-0.0934-0.00990.021-0.1235-0.0089-0.2353-13.795933.225135.1603
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|7 - A|114 A|337 - A|359 }A7 - 114
2X-RAY DIFFRACTION1{ A|7 - A|114 A|337 - A|359 }A337 - 359
3X-RAY DIFFRACTION2{ A|115 - A|336 B|1 - B|1 }A115 - 336
4X-RAY DIFFRACTION2{ A|115 - A|336 B|1 - B|1 }A1 - 362

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