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Open data
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Basic information
Entry | Database: PDB / ID: 4q2s | ||||||
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Title | Crystal Structure of S. pombe Pdc1 Ge1 Domain | ||||||
![]() | PDC1 GE1 DOMAIN | ||||||
![]() | RNA BINDING PROTEIN / Ge1 domain / P-body assembly | ||||||
Function / homology | deadenylation-independent decapping of nuclear-transcribed mRNA / P-body assembly / P-body / cytoplasmic stress granule / molecular adaptor activity / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / cytoplasm / Uncharacterized protein C20G4.08![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Noeldeke, E.R. / Neu, A. / Zocher, G. / Sprangers, R. | ||||||
![]() | ![]() Title: In vitro reconstitution of a cellular phase-transition process that involves the mRNA decapping machinery. Authors: Fromm, S.A. / Kamenz, J. / Noldeke, E.R. / Neu, A. / Zocher, G. / Sprangers, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 69.2 KB | Display | ![]() |
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PDB format | ![]() | 51.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 421.8 KB | Display | ![]() |
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Full document | ![]() | 422 KB | Display | |
Data in XML | ![]() | 7.8 KB | Display | |
Data in CIF | ![]() | 10.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 16241.898 Da / Num. of mol.: 1 / Fragment: unp residues 932-1070 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 972 / ATCC 24843 / Gene: SPAC20G4.08, SPAC4F10.01 / Production host: ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.59 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M Ammonium Acetate, 0.1 M HEPES, 25% (w/v) PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 19, 2013 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→40.4 Å / Num. all: 30393 / Num. obs: 30287 / % possible obs: 99.7 % / Observed criterion σ(I): -2 |
Reflection shell | Resolution: 1.35→1.39 Å / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: after obtaining initial molecular replacement model by S-SAD Resolution: 1.35→40.44 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.516 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.06 / 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: 19.888 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→40.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.35→1.385 Å / Total num. of bins used: 20
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