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Yorodumi- PDB-2qa4: A more complete structure of the the L7/L12 stalk of the Haloarcu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qa4 | ||||||
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Title | A more complete structure of the the L7/L12 stalk of the Haloarcula marismortui 50S large ribosomal subunit | ||||||
Components |
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Keywords | RIBOSOME / Large ribosomal subunit / Ribonucleoprotein / Ribosomal protein / RNA-binding / rRNA-binding / tRNA-binding / Metal-binding / Zinc / Zinc-finger | ||||||
Function / homology | Function and homology information ribonuclease P activity / tRNA 5'-leader removal / box C/D methylation guide snoRNP complex / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of SSU-rRNA / mRNA splicing, via spliceosome / 5S rRNA binding / large ribosomal subunit rRNA binding ...ribonuclease P activity / tRNA 5'-leader removal / box C/D methylation guide snoRNP complex / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of SSU-rRNA / mRNA splicing, via spliceosome / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / DNA repair / mRNA binding / nucleotide binding / DNA binding / zinc ion binding Similarity search - Function | ||||||
Biological species | Haloarcula marismortui (Halophile) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / CNS / Resolution: 3 Å | ||||||
Authors | Steitz, T.A. / Kavran, J.M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Structure of the base of the L7/L12 stalk of the Haloarcula marismortui large ribosomal subunit: Analysis of L11 movements Authors: Kavran, J.M. / Steitz, T.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qa4.cif.gz | 2.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2qa4.ent.gz | 1.8 MB | Display | PDB format |
PDBx/mmJSON format | 2qa4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2qa4_validation.pdf.gz | 818 KB | Display | wwPDB validaton report |
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Full document | 2qa4_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 2qa4_validation.xml.gz | 246.8 KB | Display | |
Data in CIF | 2qa4_validation.cif.gz | 353.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qa/2qa4 ftp://data.pdbj.org/pub/pdb/validation_reports/qa/2qa4 | HTTPS FTP |
-Related structure data
Related structure data | 1jj2S 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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Unit cell |
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-Components
-RNA chain , 2 types, 2 molecules 09
#1: RNA chain | Mass: 946076.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: GenBank: 3377779 |
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#2: RNA chain | Mass: 39318.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: GenBank: 3377779 |
+50S ribosomal protein ... , 28 types, 28 molecules ABCDEFHIJKLMNOPQRSTUVWXYZ123
-Protein , 1 types, 1 molecules G
#9: Protein | Mass: 37213.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P15825 |
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-Non-polymers , 5 types, 231 molecules
#32: Chemical | ChemComp-MG / #33: Chemical | #34: Chemical | ChemComp-NA / #35: Chemical | ChemComp-CL / #36: Chemical | ChemComp-CD / |
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-Details
Sequence details | RESIDUE A 1207 AND RESIDUE C 1208 CHAIN 0 ARE NOT LINKED. DISTANCE OF O3'-P BOND IS 2.51A. DISTANCE ...RESIDUE A 1207 AND RESIDUE C 1208 CHAIN 0 ARE NOT LINKED. DISTANCE OF O3'-P BOND IS 2.51A. DISTANCE OF C-N BOND BETWEEN RESIDUE G LEU 53 AND RESIDUE G HIS 54 IS 1.63A. DISTANCE OF C-N BOND BETWEEN RESIDUE G HIS 54 AND RESIDUE G GLY 55 IS 0.99A. |
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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: 3.18 Å3/Da / Density % sol: 61.31 % |
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Crystal grow | Details: PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 10, 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: 3→50 Å / Num. obs: 361885 / % possible obs: 98.2 % / Observed criterion σ(F): 1 / Redundancy: 5.6 % / Rmerge(I) obs: 0.134 / Net I/σ(I): 10 |
-Processing
Software |
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Refinement | Method to determine structure: CNS Starting model: PDB ENTRY 1JJ2 Resolution: 3→50 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 3→50 Å
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