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Yorodumi- PDB-3cpq: Crystal Structure of L30e a ribosomal protein from Methanocaldoco... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cpq | ||||||
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Title | Crystal Structure of L30e a ribosomal protein from Methanocaldococcus jannaschii DSM2661 (MJ1044) | ||||||
Components | 50S ribosomal protein L30eRibosome | ||||||
Keywords | RIBOSOMAL PROTEIN / ribosomal / RNA-protein / elongation factor / Ribonucleoprotein / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information cytosolic large ribosomal subunit / structural constituent of ribosome / translation / RNA binding Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Jeyakanthan, J. / Sarani, R. / Mridula, P. / Sekar, K. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of L30e a ribosomal protein from Methanocaldococcus jannaschii DSM2661 (MJ1044) Authors: Jeyakanthan, J. / Sarani, R. / Mridula, P. / Sekar, K. / Kuramitsu, S. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cpq.cif.gz | 52.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cpq.ent.gz | 37.9 KB | Display | PDB format |
PDBx/mmJSON format | 3cpq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cp/3cpq ftp://data.pdbj.org/pub/pdb/validation_reports/cp/3cpq | HTTPS FTP |
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-Related structure data
Related structure data | 1w41S 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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-Components
#1: Protein | Mass: 12154.249 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Strain: DSM2661 / Plasmid: PET21A / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA(DE3) / References: UniProt: P54061 #2: Water | ChemComp-HOH / | |
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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: 2.15 Å3/Da / Density % sol: 42.91 % |
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Crystal grow | Temperature: 291 K / Method: microbatch / pH: 6 Details: 40% PEG400, 0.1 MES, 5% PEG3000, pH 6.0, MICROBATCH, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jun 13, 2007 / Details: RH Coated Bent-Cyrindrical MIRROR |
Radiation | Monochromator: SI 1 1 1 DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 16282 / % possible obs: 100 % / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.088 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.478 / Num. unique all: 1595 / Rsym value: 0.541 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1W41 Resolution: 1.9→46.12 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 984491.78 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 64.0661 Å2 / ksol: 0.37649 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 26.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→46.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.99 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 8
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Xplor file |
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