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Yorodumi- PDB-5dar: CRYSTAL STRUCTURE OF THE BASE OF THE RIBOSOMAL P STALK FROM METHA... -
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-Basic information
Entry | Database: PDB / ID: 5dar | ||||||
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Title | CRYSTAL STRUCTURE OF THE BASE OF THE RIBOSOMAL P STALK FROM METHANOCOCCUS JANNASCHII | ||||||
Components |
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Keywords | RIBOSOMAL PROTEIN / ribosome / P-stalk / archaea | ||||||
Function / homology | Function and homology information large ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / structural constituent of ribosome / translation Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Gabdulkhakov, A.G. / Mitroshin, I.V. / Garber, M.B. | ||||||
Citation | Journal: To Be Published Title: CRYSTAL STRUCTURE OF THE BASE OF THE RIBOSOMAL P STALK FROM METHANOCOCCUS JANNASCHII Authors: Gabdulkhakov, A.G. / Mitroshin, I.V. / Garber, M.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dar.cif.gz | 227 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dar.ent.gz | 174.7 KB | Display | PDB format |
PDBx/mmJSON format | 5dar.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dar_validation.pdf.gz | 498.5 KB | Display | wwPDB validaton report |
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Full document | 5dar_full_validation.pdf.gz | 537.5 KB | Display | |
Data in XML | 5dar_validation.xml.gz | 33.1 KB | Display | |
Data in CIF | 5dar_validation.cif.gz | 46.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/5dar ftp://data.pdbj.org/pub/pdb/validation_reports/da/5dar | HTTPS FTP |
-Related 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
-RNA chain , 1 types, 2 molecules AD
#1: RNA chain | Mass: 23928.295 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Plasmid: pMja23S-74.UC18 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): XL1(Blue) / References: GenBank: 470491724 |
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-50S ribosomal protein ... , 2 types, 4 molecules BECF
#2: Protein | Mass: 23353.793 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Gene: rpl10, rplP0, MJ0509 / Plasmid: pET-11c/MjaP0NTF / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pUBS520 / References: UniProt: P54049 #3: Protein | Mass: 17513.326 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Gene: rpl11, MJ0373 / Plasmid: pET-11c/MjaL11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pUBS520 / References: UniProt: P54030 |
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-Non-polymers , 4 types, 30 molecules
#4: Chemical | ChemComp-MG / #5: Chemical | #6: Chemical | ChemComp-K / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.52 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 50 mM Tris-HCl, pH 7.5, 0.15 M KCl, 20 mM MgCl2, 15% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Jul 22, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→20 Å / Num. all: 25542 / Num. obs: 25542 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Redundancy: 4.35 % / Rsym value: 0.14 / Net I/σ(I): 7.01 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.09 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5COL, 5D6G Resolution: 2.9→20 Å / Cor.coef. Fo:Fc: 0.859 / Cor.coef. Fo:Fc free: 0.812 / Cross valid method: THROUGHOUT / ESU R Free: 0.521 / 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: 43.6 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→20 Å
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Refine LS restraints |
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