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Yorodumi- PDB-4ww7: Crystal structure of binary complex Bud32-Cgi121 in complex with AMP -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ww7 | ||||||
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Title | Crystal structure of binary complex Bud32-Cgi121 in complex with AMP | ||||||
Components | (EKC/KEOPS complex subunit ...) x 2 | ||||||
Keywords | TRANSFERASE / KEOPS / binary complex / Bud32-Cgi121 / tRNA t6A | ||||||
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: 1.669 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 | 4ww7.cif.gz | 101.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ww7.ent.gz | 74.3 KB | Display | PDB format |
PDBx/mmJSON format | 4ww7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ww/4ww7 ftp://data.pdbj.org/pub/pdb/validation_reports/ww/4ww7 | HTTPS FTP |
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-Related structure data
Related structure data | 4ww5C 4ww9C 4wwaC 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
-EKC/KEOPS complex subunit ... , 2 types, 2 molecules AB
#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(DE3) (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(DE3) (bacteria) / References: UniProt: Q03705 |
-Non-polymers , 4 types, 222 molecules
#3: Chemical | ChemComp-AMP / | ||||
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#4: Chemical | ChemComp-ACT / #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: 0.1 M Sodium Acetate pH 4.8, 2.0 M Ammonium Sulfate, 0.1 M NaCl, 10 mM Tris-HcL pH 7.5, 5 mM AMP and MgCl2 PH range: 4.6-4.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97911 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 14, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97911 Å / Relative weight: 1 |
Reflection | Resolution: 1.669→36.02 Å / Num. all: 236981 / Num. obs: 64292 / % possible obs: 99.4 % / Redundancy: 3.69 % / Rsym value: 0.045 / Net I/σ(I): 18.48 |
Reflection shell | Resolution: 1.669→1.729 Å / % possible all: 98.46 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine) / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Methanocaldococcus jannaschii Bud32/Cgi121 Resolution: 1.669→36.015 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 20.75 / 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: 51.191 Å2 / ksol: 0.385 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.669→36.015 Å
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Refine LS restraints |
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LS refinement shell |
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