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Yorodumi- PDB-6vzh: Structure of Human Vaccinia-related Kinase 1 (VRK1) Bound to LDSM311 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vzh | ||||||||||||
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Title | Structure of Human Vaccinia-related Kinase 1 (VRK1) Bound to LDSM311 | ||||||||||||
Components | Serine/threonine-protein kinase VRK1 | ||||||||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / protein kinase / inhibitor / Structural Genomics / Structural Genomics Consortium / SGC / TRANSFERASE-TRANSFERASE INHIBITOR / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||||||||
Function / homology | Function and homology information Golgi disassembly / histone H3T3 kinase activity / Nuclear Envelope Breakdown / positive regulation of protein localization to chromatin / mitotic nuclear membrane disassembly / Golgi stack / Initiation of Nuclear Envelope (NE) Reformation / histone H3S10 kinase activity / kinase activity / histone binding ...Golgi disassembly / histone H3T3 kinase activity / Nuclear Envelope Breakdown / positive regulation of protein localization to chromatin / mitotic nuclear membrane disassembly / Golgi stack / Initiation of Nuclear Envelope (NE) Reformation / histone H3S10 kinase activity / kinase activity / histone binding / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / cell division / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / nucleolus / protein kinase binding / signal transduction / nucleoplasm / ATP binding / nucleus / cytosol Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.55 Å | ||||||||||||
Authors | dos Reis, C.V. / Dutra, L.A. / Gama, F. / Ferreira, M. / Mascarello, A. / Azevedo, H. / Guimaraes, C. / Massirer, K.B. / Arruda, P. / Edwards, A.M. ...dos Reis, C.V. / Dutra, L.A. / Gama, F. / Ferreira, M. / Mascarello, A. / Azevedo, H. / Guimaraes, C. / Massirer, K.B. / Arruda, P. / Edwards, A.M. / Counago, R.M. / Structural Genomics Consortium (SGC) | ||||||||||||
Funding support | Brazil, 3items
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Citation | Journal: To be Published Title: Structure of Human Vaccinia-related Kinase 1 (VRK1) Bound to LDSM311 Authors: dos Reis, C.V. / Dutra, L.A. / Gama, F. / Ferreira, M. / Mascarello, A. / Azevedo, H. / Guimaraes, C.R.W. / Massirer, K.B. / Arruda, P. / Edwards, A.M. / Counago, R.M. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6vzh.cif.gz | 494.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vzh.ent.gz | 407 KB | Display | PDB format |
PDBx/mmJSON format | 6vzh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vzh_validation.pdf.gz | 407.1 KB | Display | wwPDB validaton report |
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Full document | 6vzh_full_validation.pdf.gz | 407.9 KB | Display | |
Data in XML | 6vzh_validation.xml.gz | 1.6 KB | Display | |
Data in CIF | 6vzh_validation.cif.gz | 13.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vz/6vzh ftp://data.pdbj.org/pub/pdb/validation_reports/vz/6vzh | HTTPS FTP |
-Related structure data
Related structure data | 6bruS 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 41138.125 Da / Num. of mol.: 4 Mutation: K34A,K35A,E36A,E212A,K214A,E215A,E292A,K293A,K295A,K359A,K360A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: VRK1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): R3 References: UniProt: Q99986, non-specific serine/threonine protein kinase #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | ChemComp-EDO / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.58 Å3/Da / Density % sol: 52.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 27.5% PEG3350, 300 mM lithium sulfate, 0.1 M sodium tartrate, 0.1 M Bis-Tris, 0.1 M glycylglycine, cryoprotectant: 30% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 5, 2019 | ||||||||||||||||||||||||||||||
Radiation | Monochromator: cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.55→96.3 Å / Num. obs: 56320 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.055 / Rrim(I) all: 0.142 / Net I/σ(I): 8.7 / Num. measured all: 376419 / Scaling rejects: 6 | ||||||||||||||||||||||||||||||
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 Starting model: PDB entry 6BRU Resolution: 2.55→20 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.931 / SU B: 30.444 / SU ML: 0.28 / SU R Cruickshank DPI: 0.4584 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.457 / ESU R Free: 0.278 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 143.64 Å2 / Biso mean: 63.234 Å2 / Biso min: 43.02 Å2
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Refinement step | Cycle: final / Resolution: 2.55→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.55→2.615 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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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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