+Open data
-Basic information
Entry | Database: PDB / ID: 4xah | ||||||
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Title | X-ray crystal structure of S. cerevisiae Cgi121 | ||||||
Components | EKC/KEOPS complex subunit CGI121 | ||||||
Keywords | PROTEIN BINDING / KEOPS / Cgi121 / Bud32-binding protein | ||||||
Function / homology | Function and homology information EKC/KEOPS complex / tRNA threonylcarbamoyladenosine modification / telomere maintenance via recombination / telomere maintenance / maintenance of translational fidelity / DNA recombination / chromosome, telomeric region / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å | ||||||
Authors | Zhang, W. / Graille, M. / Collinet, B. / 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 | 4xah.cif.gz | 90.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xah.ent.gz | 72.6 KB | Display | PDB format |
PDBx/mmJSON format | 4xah.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xa/4xah ftp://data.pdbj.org/pub/pdb/validation_reports/xa/4xah | HTTPS FTP |
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-Related structure data
Related structure data | 4ww5C 4ww7C 4ww9C 4wwaC 4wx8C 4wxaC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 21591.812 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: CGI121, YML036W Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q03705 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 10 mM Tris-HCl pH 7.5, 100mM NaCl, 10mM 2-mercaptoethanol,0.6 M sodium citrate, 0.05 M sodium citrate pH 5.0 PH range: 5.0 - 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.987 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 1, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. all: 115741 / Num. obs: 32377 / % possible obs: 99.3 % / Redundancy: 3.6 % / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2.5→2.57 Å / Redundancy: 3.5 % / % possible all: 99.3 |
-Processing
Software |
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Refinement | Resolution: 2.5→20 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 24.47 / 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: 67.763 Å2 / ksol: 0.357 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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LS refinement shell |
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