+Open data
-Basic information
Entry | Database: PDB / ID: 4eba | ||||||
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Title | Crystal structure of the Rna14-Rna15 complex | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN/RNA BINDING PROTEIN / HAT domain / HEAT repeat / monkeytail / Clp1 / Pcf11 / STRUCTURAL PROTEIN-RNA BINDING PROTEIN complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Kluyveromyces lactis (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||
Authors | Paulson, A.R. / Tong, L. | ||||||
Citation | Journal: Rna / Year: 2012 Title: Crystal structure of the Rna14-Rna15 complex. Authors: Paulson, A.R. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4eba.cif.gz | 733.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4eba.ent.gz | 603.5 KB | Display | PDB format |
PDBx/mmJSON format | 4eba.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eb/4eba ftp://data.pdbj.org/pub/pdb/validation_reports/eb/4eba | HTTPS FTP |
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-Related structure data
Related structure data | 4e6hC 4e85SC 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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3 |
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Unit cell |
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Details | The trimers are formed by two Rna14 and one Rna15. |
-Components
#1: Protein | Mass: 76161.523 Da / Num. of mol.: 6 / Fragment: UNP residues 18-661 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Kluyveromyces lactis (yeast) Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 Gene: RNA14, KLLA0F26290g / Production host: Escherichia coli (E. coli) / References: UniProt: Q6CII8 #2: Protein | Mass: 19549.305 Da / Num. of mol.: 3 / Fragment: UNP residues 105-258 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Kluyveromyces lactis (yeast) Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 Gene: KLLA0F09383g / Production host: Escherichia coli (E. coli) / References: UniProt: Q6CKN2 |
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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: 2.61 Å3/Da / Density % sol: 52.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 50 mM HEPES 7.0, 1% tryptone, 13% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 / Wavelength: 1.075 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 9, 2011 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→50 Å / Num. all: 79000 / Num. obs: 71640 / % possible obs: 90.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 1.7 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 10.9049 |
Reflection shell | Resolution: 3.3→3.42 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 1.242 / % possible all: 71.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4E85 Resolution: 3.3→47.79 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 371325.06 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 57.2895 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 100.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.3→47.79 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.3→3.42 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 10
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Xplor file | Serial no: 1 / Param file: protein_rep.param / Topol file: protein.top |