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Yorodumi- PDB-4u3y: Apo Mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4) -
+Open data
-Basic information
Entry | Database: PDB / ID: 4u3y | ||||||
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Title | Apo Mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4) | ||||||
Components | Mitogen-activated protein kinase kinase kinase kinase 4 | ||||||
Keywords | TRANSFERASE / kinase | ||||||
Function / homology | Function and homology information positive regulation of ARF protein signal transduction / creatine kinase activity / positive regulation of keratinocyte migration / positive regulation of focal adhesion disassembly / negative regulation of cell-matrix adhesion / positive regulation of focal adhesion assembly / regulation of MAPK cascade / regulation of JNK cascade / neuron projection morphogenesis / positive regulation of GTPase activity ...positive regulation of ARF protein signal transduction / creatine kinase activity / positive regulation of keratinocyte migration / positive regulation of focal adhesion disassembly / negative regulation of cell-matrix adhesion / positive regulation of focal adhesion assembly / regulation of MAPK cascade / regulation of JNK cascade / neuron projection morphogenesis / positive regulation of GTPase activity / MAPK cascade / microtubule binding / Oxidative Stress Induced Senescence / non-specific serine/threonine protein kinase / positive regulation of cell migration / intracellular signal transduction / protein phosphorylation / focal adhesion / protein serine kinase activity / protein serine/threonine kinase activity / negative regulation of apoptotic process / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.45 Å | ||||||
Authors | Harris, S.F. / Wu, P. / Coons, M. | ||||||
Citation | Journal: to be published Title: Structural Plasticity and Kinase Activation in a Cohort of MAP4K4 Structures Authors: Wu, P. / Chen, H. / Coons, M. / Crawford, T.D. / Kirkpatrick, D.S. / Murray, L. / Ndubaku, C.O. / Nonomiya, J. / Pham, V. / Schmidt, S. / Smysczek, T. / Vitorino, P. / Ye, W. / Harris, S.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4u3y.cif.gz | 149.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4u3y.ent.gz | 115.5 KB | Display | PDB format |
PDBx/mmJSON format | 4u3y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u3/4u3y ftp://data.pdbj.org/pub/pdb/validation_reports/u3/4u3y | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 37870.078 Da / Num. of mol.: 2 / Fragment: kinase domain (UNP residues 2-328) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAP4K4, HGK, KIAA0687, NIK / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 References: UniProt: O95819, non-specific serine/threonine protein kinase #2: Chemical | ChemComp-DMS / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.32 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.3 / Details: 0.2 M potassium citrate, pH 8.3, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 20, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: DOUBLE CRYSTAL Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.45→30 Å / Num. obs: 108043 / % possible obs: 100 % / Redundancy: 7.2 % / Biso Wilson estimate: 17.86 Å2 / Rmerge(I) obs: 0.062 / Χ2: 1.183 / Net I/av σ(I): 29.727 / Net I/σ(I): 12.7 / Num. measured all: 779291 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0 / % possible all: 100
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.45→28.93 Å / Cor.coef. Fo:Fc: 0.9617 / Cor.coef. Fo:Fc free: 0.9529 / SU R Cruickshank DPI: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.071 / SU Rfree Blow DPI: 0.071 / SU Rfree Cruickshank DPI: 0.068
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Displacement parameters | Biso max: 124.86 Å2 / Biso mean: 23.83 Å2 / Biso min: 7.23 Å2
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Refine analyze | Luzzati coordinate error obs: 0.163 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.45→28.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.49 Å / Total num. of bins used: 20
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