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- PDB-3cc2: The Refined Crystal Structure of the Haloarcula Marismortui Large... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3cc2 | ||||||
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Title | The Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution with rrnA Sequence for the 23S rRNA and Genome-derived Sequences for r-Proteins | ||||||
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![]() | RIBOSOME / genomic sequnece for r-proteins / Ribonucleoprotein / Ribosomal protein / RNA-binding / rRNA-binding / tRNA-binding / Metal-binding / Zinc-finger | ||||||
Function / homology | ![]() ribonuclease P activity / tRNA 5'-leader removal / box C/D methylation guide snoRNP complex / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / mRNA splicing, via spliceosome / 5S rRNA binding ...ribonuclease P activity / tRNA 5'-leader removal / box C/D methylation guide snoRNP complex / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / mRNA splicing, via spliceosome / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / DNA repair / nucleotide binding / mRNA binding / DNA binding / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Gurel, G. / Blaha, G. | ||||||
![]() | ![]() Title: Mutations outside the anisomycin-binding site can make ribosomes drug-resistant. Authors: Blaha, G. / Gurel, G. / Schroeder, S.J. / Moore, P.B. / Steitz, T.A. #1: ![]() Title: The roles of ribosomal proteins in the structure assembly, and evolution of the large ribosomal subunit. Authors: Klein, D.J. / Moore, P.B. / Steitz, T.A. #2: Journal: Genome Res. / Year: 2004 Title: Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea. Authors: Baliga, N.S. / Bonneau, R. / Facciotti, M.T. / Pan, M. / Glusman, G. / Deutsch, E.W. / Shannon, P. / Chiu, Y. / Weng, R.S. / Gan, R.R. / Hung, P. / Date, S.V. / Marcotte, E. / Hood, L. / Ng, W.V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 2.5 MB | Display | ![]() |
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PDB format | ![]() | 1.9 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 661 KB | Display | ![]() |
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Full document | ![]() | 828.1 KB | Display | |
Data in XML | ![]() | 124.1 KB | Display | |
Data in CIF | ![]() | 246.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3cc4C ![]() 3cc7C ![]() 3cceC ![]() 3ccjC ![]() 3cclC ![]() 3ccmC ![]() 3ccqC ![]() 3ccrC ![]() 3ccsC ![]() 3ccuC ![]() 3ccvC ![]() 3cd6C C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
+50S ribosomal protein ... , 29 types, 29 molecules ABCDEFGHIJKLMNOPQRSTUVWXYZ123
-RNA chain , 2 types, 2 molecules 09
#30: RNA chain | Mass: 946463.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#31: RNA chain | Mass: 39303.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Non-polymers , 6 types, 8054 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/CD.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/CD.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
#32: Chemical | ChemComp-MG / #33: Chemical | ChemComp-NA / #34: Chemical | ChemComp-CL / #35: Chemical | ChemComp-CD / #36: Chemical | #37: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE SEQUENCE OF CHAIN 0 MATCHES TO GB ENTRY AY596297 BETWEEN 2634210 AND 2637132. THE SEQUENCE OF ...THE SEQUENCE OF CHAIN 0 MATCHES TO GB ENTRY AY596297 BETWEEN 2634210 AND 2637132. THE SEQUENCE OF CHAIN Z MATCHES TO REFSEQ ENTRY YP_136287. |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.02 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: sitting drop / pH: 5.8 Details: PEG6000, KCL, NH4CL, MGCl2, pH 5.80, sitting drop, temperature 292K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.4→90 Å / Num. obs: 666819 / % possible obs: 95.6 % / Redundancy: 9.1 % / Biso Wilson estimate: 35.7 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 26.6 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 29.3588 Å2 / ksol: 0.322344 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→49.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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