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Open data
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Basic information
Entry | Database: PDB / ID: 4wx8 | ||||||
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Title | Crystal structure of binary complex Gon7-Pcc1 | ||||||
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![]() | CELL CYCLE / KEOPS / Gon7-Pcc1 / tRNA t6A | ||||||
Function / homology | ![]() tRNA threonylcarbamoyladenosine metabolic process / EKC/KEOPS complex / tRNA threonylcarbamoyladenosine modification / cell wall mannoprotein biosynthetic process / telomere maintenance via recombination / telomere maintenance / maintenance of translational fidelity / chromatin DNA binding / chromosome, telomeric region / molecular adaptor activity ...tRNA threonylcarbamoyladenosine metabolic process / EKC/KEOPS complex / tRNA threonylcarbamoyladenosine modification / cell wall mannoprotein biosynthetic process / telomere maintenance via recombination / telomere maintenance / maintenance of translational fidelity / chromatin DNA binding / chromosome, telomeric region / molecular adaptor activity / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Zhang, W. / Van Tilbeurgh, H. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 168.4 KB | Display | ![]() |
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PDB format | ![]() | 139.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 481 KB | Display | ![]() |
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Full document | ![]() | 487.6 KB | Display | |
Data in XML | ![]() | 16.8 KB | Display | |
Data in CIF | ![]() | 22.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ww5C ![]() 4ww7C ![]() 4ww9C ![]() 4wwaC ![]() 4wxaC ![]() 4xahC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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3 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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Components
#1: Protein | Mass: 10975.087 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: PCC1, YKR095W-A Production host: ![]() ![]() References: UniProt: Q3E833 #2: Protein | Mass: 13763.696 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: GON7, LDB6, PCC2, YJL184W, J0420 Production host: ![]() ![]() References: UniProt: P46984 #3: Chemical | ChemComp-ACT / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M Sodium Acetate pH 6.5, 20% PEG1500, 20% Glycerol, 3% Methanol PH range: 6.0-7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97895 Å / Relative weight: 1 |
Reflection | Resolution: 2.99→43.53 Å / Num. obs: 13327 / % possible obs: 99.54 % / Redundancy: 3.83 % / Net I/σ(I): 8.08 |
Reflection shell | Resolution: 2.992→3.099 Å / % possible all: 97.5 |
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Processing
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Refinement | Resolution: 2.99→43.53 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.883 / SU B: 42.091 / SU ML: 0.399 / Cross valid method: THROUGHOUT / ESU R: 2.274 / ESU R Free: 0.463 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: 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 mean: 66.138 Å2
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Refinement step | Cycle: 1 / Resolution: 2.99→43.53 Å
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Refine LS restraints |
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