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- PDB-2jkd: Structure of the yeast Pml1 splicing factor and its integration i... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2jkd | ||||||
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Title | Structure of the yeast Pml1 splicing factor and its integration into the RES complex | ||||||
![]() | PRE-MRNA LEAKAGE PROTEIN 1 | ||||||
![]() | GENE REGULATION / MRNA PROCESSING / PML1/SNU17/BUD13 / PRE-MRNA SPLICING / SACCHAROMYCES CEREVISIAE / PHOSPHO-PEPTIDE RECOGNITION / RES / NUCLEUS / MRNA SPLICING | ||||||
Function / homology | ![]() maintenance of RNA location / RES complex / U2-type prespliceosome assembly / U2 snRNP / mRNA export from nucleus / spliceosomal complex / mRNA splicing, via spliceosome / mRNA binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Brooks, M.A. / Dziembowski, A. / Quevillon-Cheruel, S. / Henriot, V. / Faux, C. / van Tilbeurgh, H. / Seraphin, B. | ||||||
![]() | ![]() Title: Structure of the Yeast Pml1 Splicing Factor and its Integration Into the Res Complex Authors: Brooks, M.A. / Dziembowski, A. / Quevillon-Cheruel, S. / Henriot, V. / Faux, C. / Van Tilbeurgh, H. / Seraphin, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 73 KB | Display | ![]() |
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PDB format | ![]() | 55 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.671, -0.7413, 0.0138), Vector: |
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Components
#1: Protein | Mass: 21543.215 Da / Num. of mol.: 2 / Fragment: FHA DOMAIN, RESIDUES 25-204 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: S288C / Plasmid: PET9 / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | RESIDUES 24-48 AND 113-121 OF CHAIN A AND 24-50 AND 112-121 OF CHAIN B WERE NOT MODELLED IN THE ...RESIDUES 24-48 AND 113-121 OF CHAIN A AND 24-50 AND 112-121 OF CHAIN B WERE NOT MODELLED IN THE STRUCTURE DUE TO LACK OF DENSITY. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.22 % / Description: NONE |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1M TRIS-HCL, PH 8.5, 0.2 M LISO4 AND FROM 20 TO 30% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Aug 31, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 14550 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 2.94 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 2.98 % / Rmerge(I) obs: 0.225 / Mean I/σ(I) obs: 5.82 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NONE Resolution: 2.5→40.86 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.917 / SU B: 17.602 / SU ML: 0.191 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.426 / ESU R Free: 0.281 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.84 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→40.86 Å
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Refine LS restraints |
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