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Yorodumi- PDB-3zef: Crystal structure of Prp8:Aar2 complex: second crystal form at 3.... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zef | ||||||
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Title | Crystal structure of Prp8:Aar2 complex: second crystal form at 3.1 Angstrom resolution | ||||||
Components |
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Keywords | TRANSLATION / PRE-MRNA SPLICING / SPLICEOSOME / U5 SNRNP | ||||||
Function / homology | Function and homology information generation of catalytic spliceosome for second transesterification step / mRNA 3'-splice site recognition / mRNA 5'-splice site recognition / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / spliceosomal snRNP assembly / U6 snRNA binding / pre-mRNA intronic binding ...generation of catalytic spliceosome for second transesterification step / mRNA 3'-splice site recognition / mRNA 5'-splice site recognition / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / spliceosomal snRNP assembly / U6 snRNA binding / pre-mRNA intronic binding / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / spliceosomal complex / mRNA splicing, via spliceosome / metallopeptidase activity / mRNA binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Galej, W.P. / Oubridge, C. / Newman, A.J. / Nagai, K. | ||||||
Citation | Journal: Nature / Year: 2013 Title: Crystal Structure of Prp8 Reveals Active Site Cavity of the Spliceosome Authors: Galej, W.P. / Oubridge, C. / Newman, A.J. / Nagai, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zef.cif.gz | 714.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zef.ent.gz | 575.8 KB | Display | PDB format |
PDBx/mmJSON format | 3zef.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ze/3zef ftp://data.pdbj.org/pub/pdb/validation_reports/ze/3zef | HTTPS FTP |
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-Related structure data
Related structure data | 4i43C 2og4S 3sbtS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 41734.688 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Plasmid: PRS424 / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain (production host): BCY123 / References: UniProt: P32357 #2: Protein | Mass: 176632.312 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Plasmid: PRS426 / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain (production host): BCY123 / References: UniProt: P33334 Sequence details | THE DEPOSITED SEQUENCE REPRESENTS RESIDUES 885-2414 OF THE GENBANK DATABASE ENTRY WITH MUTATIONS ...THE DEPOSITED SEQUENCE REPRESENTS | |
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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: 2.75 Å3/Da / Density % sol: 0.55 % Description: 3SBT SEPARATED INTO SINGLE CHAINS FOR MR SEARCH |
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Crystal grow | pH: 7.9 Details: 7-9% PEG 8000, 100 MM NA-CITRATE PH 7.9, 50-200 MM AMMONIUM SULFATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 6, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→137.5 Å / Num. obs: 97506 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 3.1→3.15 Å / Redundancy: 5.2 % / Rmerge(I) obs: 1.3 / Mean I/σ(I) obs: 1.4 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 3SBT, 2OG4 Resolution: 3.1→137.45 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.886 / SU B: 25.665 / SU ML: 0.441 / Cross valid method: THROUGHOUT / ESU R Free: 0.489 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES ARE REFINED INDIVIDUALLY
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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: 95.693 Å2
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Refinement step | Cycle: LAST / Resolution: 3.1→137.45 Å
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Refine LS restraints |
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