+Open data
-Basic information
Entry | Database: PDB / ID: 4wwa | ||||||
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Title | Crystal structure of binary complex Bud32-Cgi121 | ||||||
Components |
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Keywords | TRANSFERASE / KEOPS / binary complex / Bud32-Cgi121 / tRNA t6A / hydrolase | ||||||
Function / homology | Function and homology information tRNA threonylcarbamoyladenosine metabolic process / EKC/KEOPS complex / tRNA threonylcarbamoyladenosine modification / cellular bud site selection / Hydrolases; Acting on acid anhydrides / telomere maintenance via recombination / telomere maintenance / maintenance of translational fidelity / DNA recombination / chromosome, telomeric region ...tRNA threonylcarbamoyladenosine metabolic process / EKC/KEOPS complex / tRNA threonylcarbamoyladenosine modification / cellular bud site selection / Hydrolases; Acting on acid anhydrides / telomere maintenance via recombination / telomere maintenance / maintenance of translational fidelity / DNA recombination / chromosome, telomeric region / non-specific serine/threonine protein kinase / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.953 Å | ||||||
Authors | Zhang, W. / van Tilbeurgh, H. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2015 Title: Crystal structures of the Gon7/Pcc1 and Bud32/Cgi121 complexes provide a model for the complete yeast KEOPS complex. Authors: Zhang, W. / Collinet, B. / Graille, M. / Daugeron, M.C. / Lazar, N. / Libri, D. / Durand, D. / van Tilbeurgh, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wwa.cif.gz | 85.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wwa.ent.gz | 66.1 KB | Display | PDB format |
PDBx/mmJSON format | 4wwa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ww/4wwa ftp://data.pdbj.org/pub/pdb/validation_reports/ww/4wwa | HTTPS FTP |
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-Related structure data
Related structure data | 4ww5C 4ww7C 4ww9C 4wx8C 4wxaC 4xahC C: citing same article (ref.) |
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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: 29982.377 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: BUD32, LDB14, YGR262C Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P53323, Hydrolases; Acting on acid anhydrides, non-specific serine/threonine protein kinase | ||
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#2: Protein | Mass: 21515.695 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: CGI121, YML036W Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q03705 | ||
#3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.1 M Sodium Acetate pH 4.6, 2.0 M Ammounium Sulfate, 0.1 M NaCl and 10 mM Tris-HCl pH 7.5 PH range: 4.6-5.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97918 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→43.2 Å / Num. obs: 11205 / % possible obs: 99.8 % / Redundancy: 4.58 % / Rsym value: 0.124 / Net I/σ(I): 14.32 |
Reflection shell | Resolution: 2.953→3.059 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.953→43.2 Å / SU ML: 0.56 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 31.22 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.467 Å2 / ksol: 0.349 e/Å3 | |||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.953→43.2 Å
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Refine LS restraints |
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LS refinement shell |
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