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- PDB-3iab: Crystal structure of RNase P /RNase MRP proteins Pop6, Pop7 in a ... -
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Basic information
Entry | Database: PDB / ID: 3iab | ||||||
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Title | Crystal structure of RNase P /RNase MRP proteins Pop6, Pop7 in a complex with the P3 domain of RNase MRP RNA | ||||||
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![]() | HYDROLASE/RNA / RNase P / RNase MRP / Ribonuclease P / Ribonuclease MRP / Pop6 / Pop6p / Pop7 / Pop7p / P3 / NME1 / yeast / tRNA / pre-tRNA / rRNA / Ribozyme / PROTEIN-RNA COMPLEX / ALBA / heterodimer / Coiled coil / Hydrolase / Nucleus / rRNA processing / tRNA processing / Phosphoprotein / HYDROLASE-RNA COMPLEX | ||||||
Function / homology | ![]() nuclear-transcribed mRNA catabolic process, RNase MRP-dependent / intronic box C/D snoRNA processing / nucleolar ribonuclease P complex / ribonuclease MRP complex / ribonuclease P / ribonuclease P activity / rRNA primary transcript binding / tRNA 5'-leader removal / telomerase holoenzyme complex / tRNA processing ...nuclear-transcribed mRNA catabolic process, RNase MRP-dependent / intronic box C/D snoRNA processing / nucleolar ribonuclease P complex / ribonuclease MRP complex / ribonuclease P / ribonuclease P activity / rRNA primary transcript binding / tRNA 5'-leader removal / telomerase holoenzyme complex / tRNA processing / maturation of 5.8S rRNA / rRNA processing / RNA binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Perederina, A. / Esakova, O.A. / Quan, C. / Khanova, E. / Krasilnikov, A.S. | ||||||
![]() | ![]() Title: Eukaryotic ribonucleases P/MRP: the crystal structure of the P3 domain Authors: Perederina, A. / Esakova, O. / Quan, C. / Khanova, E. / Krasilnikov, A.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 87.1 KB | Display | ![]() |
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PDB format | ![]() | 69.3 KB | Display | ![]() |
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-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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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 18440.576 Da / Num. of mol.: 1 / Fragment: Pop6 / Mutation: L141M Source method: isolated from a genetically manipulated source Details: Co-expression with Pop7 Source: (gene. exp.) ![]() ![]() Gene: POP6, YGR030C / Plasmid: 762 / Production host: ![]() ![]() | ||||
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#2: Protein | Mass: 15984.972 Da / Num. of mol.: 1 / Fragment: Pop7 / Mutation: none Source method: isolated from a genetically manipulated source Details: Co-expression with Pop6 Source: (gene. exp.) ![]() ![]() Gene: POP7, RPP2, YBR1219, YBR167C / Plasmid: 762 / Production host: ![]() ![]() | ||||
#3: RNA chain | Mass: 14828.875 Da / Num. of mol.: 1 / Fragment: P3 domain Mutation: circular permutation; A49C, A50C, U59G, U60G (yeast sequence numbering). See important note regarging nucleotide numbering in the model. Source method: obtained synthetically Details: In vitro transcription; circular permutation of naturally occurring sequence. References: ribonuclease P | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | THE MODEL INCLUDES NUCLEOTIDES 29-50 AND 59-79 OF THE ORIGINAL YEAST P3 DOMAIN. THE CRYSTALLIZED ...THE MODEL INCLUDES NUCLEOTIDE | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.12 Å3/Da / Density % sol: 60.55 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.8 Details: 2M Ammonium Sulfate, 200 mM Potassium Chloride, 2% PEG 400, 5% D-trehalose, 2 mM Zinc Chloride, 5 mM Magnesium Chloride, 100 mM HEPES-Na, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 28, 2009 / Details: mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. all: 17601 / Num. obs: 16350 / % possible obs: 92.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 82.1 Å2 / Rmerge(I) obs: 0.057 |
Reflection shell | Resolution: 2.7→2.76 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 2 / Num. unique all: 934 / % possible all: 93.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: none Resolution: 2.7→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: Residues 1-3, 122-128 in Pop6 (chain A) and residues 1-13, 105-124 in Pop7 (chain B) are disordered
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Displacement parameters | Biso mean: 89.9 Å2
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Refine analyze | Luzzati coordinate error obs: 0.68 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.774 Å
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