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Yorodumi- PDB-6z5a: Crystal structure of haspin (GSG2) in complex with macrocycle ODS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6z5a | ||||||
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Title | Crystal structure of haspin (GSG2) in complex with macrocycle ODS2002941 | ||||||
Components | Serine/threonine-protein kinase haspin | ||||||
Keywords | TRANSFERASE / kinase / kinase inhibitor / haspin / gsg2 macrocycle / nanocyclic / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information histone H3T3 kinase activity / protein localization to chromosome, centromeric region / mitotic sister chromatid cohesion / mitotic spindle assembly checkpoint signaling / spindle / chromosome / mitotic cell cycle / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction ...histone H3T3 kinase activity / protein localization to chromosome, centromeric region / mitotic sister chromatid cohesion / mitotic spindle assembly checkpoint signaling / spindle / chromosome / mitotic cell cycle / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / centrosome / nucleoplasm / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Chaikuad, A. / Benderitter, P. / Hoflack, J. / Denis, A. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To Be Published Title: Crystal structure of haspin (GSG2) in complex with macrocycle ODS2002941 Authors: Chaikuad, A. / Benderitter, P. / Hoflack, J. / Denis, A. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6z5a.cif.gz | 169.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6z5a.ent.gz | 130.1 KB | Display | PDB format |
PDBx/mmJSON format | 6z5a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z5/6z5a ftp://data.pdbj.org/pub/pdb/validation_reports/z5/6z5a | HTTPS FTP |
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-Related structure data
Related structure data | 4qtcS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 40711.484 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HASPIN, GSG2 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -R3-pRARE2 References: UniProt: Q8TF76, non-specific serine/threonine protein kinase |
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-Non-polymers , 6 types, 516 molecules
#2: Chemical | #3: Chemical | ChemComp-ZN / | #4: Chemical | ChemComp-DMS / | #5: Chemical | ChemComp-NA / | #6: Chemical | ChemComp-Q8B / | #7: Water | ChemComp-HOH / | |
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-Details
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: 3.11 Å3/Da / Density % sol: 60.49 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 60.0% MPD, 0.1M SPG pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 13, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.55→57.013 Å / Num. obs: 74138 / % possible obs: 99.7 % / Redundancy: 5 % / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.046 / Rrim(I) all: 0.104 / Net I/av σ(I): 6.9 / Net I/σ(I): 10 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4qtc Resolution: 1.55→34.97 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.278 / SU ML: 0.043 / SU R Cruickshank DPI: 0.0604 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 59.96 Å2 / Biso mean: 13.897 Å2 / Biso min: 4.37 Å2
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Refinement step | Cycle: final / Resolution: 1.55→34.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 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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