+Open data
-Basic information
Entry | Database: PDB / ID: 1g62 | ||||||
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Title | CRYSTAL STRUCTURE OF S.CEREVISIAE EIF6 | ||||||
Components | RIBOSOME ANTI-ASSOCIATION FACTOR EIF6 | ||||||
Keywords | TRANSLATION / alpha-beta barrel / velcro closure / subdomain / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of 5.8S rRNA / ribosomal subunit export from nucleus / ribosomal large subunit binding / preribosome, large subunit precursor / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / translation initiation factor activity / assembly of large subunit precursor of preribosome ...maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of 5.8S rRNA / ribosomal subunit export from nucleus / ribosomal large subunit binding / preribosome, large subunit precursor / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / translation initiation factor activity / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / rRNA processing / nucleolus / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Groft, C.M. / Beckmann, R. / Sali, A. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2000 Title: Crystal structures of ribosome anti-association factor IF6. Authors: Groft, C.M. / Beckmann, R. / Sali, A. / Burley, S.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g62.cif.gz | 52.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g62.ent.gz | 37.5 KB | Display | PDB format |
PDBx/mmJSON format | 1g62.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g6/1g62 ftp://data.pdbj.org/pub/pdb/validation_reports/g6/1g62 | HTTPS FTP |
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-Related structure data
Related structure data | 1g61SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24156.150 Da / Num. of mol.: 1 / Mutation: RESIDUES 1-224 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: TIF6 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q12522 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.25 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 2M Ammonium Sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 24.0K |
Crystal | *PLUS Density % sol: 55 % |
Crystal grow | *PLUS |
Components of the solutions | *PLUS Conc.: 2 M / Common name: ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jul 4, 2000 |
Radiation | Monochromator: Copper / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→25 Å / Num. all: 9926 / Num. obs: 9926 / % possible obs: 96.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 41.3 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 2.5→25 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.34 / Num. unique all: 836 / % possible all: 84.9 |
Reflection | *PLUS Lowest resolution: 25 Å / Num. measured all: 60623 |
Reflection shell | *PLUS % possible obs: 84.9 % / Rmerge(I) obs: 0.34 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1G61 Resolution: 2.5→25 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: CNS-defined values
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Refinement step | Cycle: LAST / Resolution: 2.5→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→25 Å
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 25 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.197 / Rfactor Rfree: 0.25 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.4 | ||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 25 Å / Rfactor Rfree: 0.25 / Rfactor Rwork: 0.197 |