+Open data
-Basic information
Entry | Database: PDB / ID: 3pg1 | ||||||
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Title | MAP kinase LmaMPK10 from Leishmania major (1.95 angs resolution) | ||||||
Components | Mitogen-activated protein kinase, putative (Map kinase-like protein) | ||||||
Keywords | TRANSFERASE / ePK ser/thr protein kinase fold / ser/thr protein kinase | ||||||
Function / homology | Function and homology information MAP kinase activity / intracellular signal transduction / phosphorylation / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Leishmania major (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å | ||||||
Authors | Horjales, S. / Buschiazzo, A. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pg1.cif.gz | 155.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pg1.ent.gz | 123.3 KB | Display | PDB format |
PDBx/mmJSON format | 3pg1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pg/3pg1 ftp://data.pdbj.org/pub/pdb/validation_reports/pg/3pg1 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 41429.352 Da / Num. of mol.: 1 / Fragment: N-terminal (UNP residues 1-361) Source method: isolated from a genetically manipulated source Details: The plasmid has been modified including a N-terminal His-tag cleavable with TEV protease Source: (gene. exp.) Leishmania major (eukaryote) / Gene: LmjF10.0200 / Plasmid: pQE80 / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 F / References: UniProt: Q4QHJ8 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 12% PEG 4000, 0.1M Hepes, 4% isopropanol, 5% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 108 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 4, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Varimax-HF multilayer mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.95→28.73 Å / Num. all: 31659 / Num. obs: 31659 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rsym value: 0.05 / Net I/σ(I): 15.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→28.73 Å / Cor.coef. Fo:Fc: 0.9482 / Cor.coef. Fo:Fc free: 0.9338 / Occupancy max: 1 / Occupancy min: 0.5 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: TLS WAS USED, WITH TWO GROUPS
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Displacement parameters | Biso max: 140.77 Å2 / Biso mean: 53.6331 Å2 / Biso min: 15.04 Å2
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Refine analyze | Luzzati coordinate error obs: 0.254 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→28.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.01 Å / Total num. of bins used: 16
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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