+Open data
-Basic information
Entry | Database: PDB / ID: 4uy9 | ||||||
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Title | Structure of MLK1 kinase domain with leucine zipper 1 | ||||||
Components | MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 9 | ||||||
Keywords | TRANSFERASE / MLK FAMILY / MLK1 AND MLK3 SUBTYPE / ATP-BINDING / KINASE / NUCLEOTIDE-BINDING / PHOSPHOPROTEIN / SERINE/THREONINE-PROTEIN KINASE / SH3 DOMAIN | ||||||
Function / homology | Function and homology information mitogen-activated protein kinase kinase kinase / JUN kinase kinase kinase activity / MAP kinase kinase activity / protein autophosphorylation / positive regulation of apoptotic process / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / protein homodimerization activity / ATP binding Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å | ||||||
Authors | Read, J.A. / Brassington, C. / Pollard, H.K. / Phillips, C. / Green, I. / Overmann, R. / Collier, M. | ||||||
Citation | Journal: Cancer Res. / Year: 2016 Title: Recurrent Mlk4 Loss-of-Function Mutations Suppress Jnk Signaling to Promote Colon Tumorigenesis. Authors: Marusiak, A.A. / Stephenson, N.L. / Baik, H. / Trotter, E.W. / Li, Y. / Blyth, K. / Mason, S. / Chapman, P. / Puto, L.A. / Read, J.A. / Brassington, C. / Pollard, H.K. / Phillips, C. / ...Authors: Marusiak, A.A. / Stephenson, N.L. / Baik, H. / Trotter, E.W. / Li, Y. / Blyth, K. / Mason, S. / Chapman, P. / Puto, L.A. / Read, J.A. / Brassington, C. / Pollard, H.K. / Phillips, C. / Green, I. / Overman, R. / Collier, M. / Testoni, E. / Miller, C. / Hunter, T. / Sansom, O.J. / Brognard, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4uy9.cif.gz | 257 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uy9.ent.gz | 209.9 KB | Display | PDB format |
PDBx/mmJSON format | 4uy9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uy/4uy9 ftp://data.pdbj.org/pub/pdb/validation_reports/uy/4uy9 | HTTPS FTP |
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-Related structure data
Related structure data | 4uyaC 3dtcS C: citing same article (ref.) S: Starting model for refinement |
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Similar 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: 36616.129 Da / Num. of mol.: 2 Fragment: KINASE DOMAIN WITH N-TERMINAL LEUCINE ZIPPER 1, RESIDUES 135-456 Source method: isolated from a genetically manipulated source Details: PROTEIN DEPHOSPHORYLATED / Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) References: UniProt: P80192, mitogen-activated protein kinase kinase kinase #2: 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: 3.86 Å3/Da / Density % sol: 68.17 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 29, 2013 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→78 Å / Num. obs: 29688 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 12.5 % / Biso Wilson estimate: 91.25 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 2.8→3 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 2.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3DTC Resolution: 2.81→77.87 Å / Cor.coef. Fo:Fc: 0.9405 / Cor.coef. Fo:Fc free: 0.9212 / SU R Cruickshank DPI: 0.375 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.415 / SU Rfree Blow DPI: 0.267 / SU Rfree Cruickshank DPI: 0.262
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Displacement parameters | Biso mean: 77.68 Å2
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Refine analyze | Luzzati coordinate error obs: 0.42 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.81→77.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.81→2.91 Å / Total num. of bins used: 15
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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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