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Yorodumi- PDB-4r3e: Structure of the spliceosomal peptidyl-prolyl cis-trans isomerase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4r3e | ||||||
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Title | Structure of the spliceosomal peptidyl-prolyl cis-trans isomerase Cwc27 from Homo sapiens | ||||||
Components | Peptidyl-prolyl cis-trans isomerase CWC27 homolog | ||||||
Keywords | ISOMERASE / Cyclophilin-type PPIase / nucleus | ||||||
Function / homology | Function and homology information U2-type precatalytic spliceosome / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / mRNA splicing, via spliceosome / protein folding / nucleoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Ulrich, A. / Wahl, M.C. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Structure and evolution of the spliceosomal peptidyl-prolyl cis-trans isomerase Cwc27. Authors: Ulrich, A. / Wahl, M.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4r3e.cif.gz | 53.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4r3e.ent.gz | 37.4 KB | Display | PDB format |
PDBx/mmJSON format | 4r3e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r3/4r3e ftp://data.pdbj.org/pub/pdb/validation_reports/r3/4r3e | HTTPS FTP |
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-Related structure data
Related structure data | 4r3fC 2hq6S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20133.549 Da / Num. of mol.: 1 / Fragment: N-terminal fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CWC27, SDCCAG10, UNQ438/PRO871 / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta / References: UniProt: Q6UX04, peptidylprolyl isomerase | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | PROTEOLYSIS HAPPENED DURING CRYSTALLIZATION AND THE AUTHORS ARE ARE NOT SURE WHERE THE ENZYMATIC ...PROTEOLYSI | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.7 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1 M magnesium formate 15% PEG 3,350, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Sep 14, 2012 |
Radiation | Monochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 2→44.27 Å / Num. obs: 30399 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 30.5 Å2 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 2114 / % possible all: 93.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2HQ6 Resolution: 2→44.27 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.796 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.144 / 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: 25.43 Å2
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Refinement step | Cycle: LAST / Resolution: 2→44.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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