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Yorodumi- PDB-1feu: CRYSTAL STRUCTURE OF RIBOSOMAL PROTEIN TL5, ONE OF THE CTC FAMILY... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1feu | ||||||
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Title | CRYSTAL STRUCTURE OF RIBOSOMAL PROTEIN TL5, ONE OF THE CTC FAMILY PROTEINS, COMPLEXED WITH A FRAGMENT OF 5S RRNA. | ||||||
Components |
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Keywords | RIBOSOME / general stress protein CTC / 5S rRNA-protein complex / cadmium ions | ||||||
Function / homology | Function and homology information 5S rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å | ||||||
Authors | Fedorov, R.V. / Meshcheryakov, V.A. / Gongadze, G.M. / Fomenkova, N.P. / Nevskaya, N.A. / Selmer, M. / Laurberg, M. / Kristensen, O. / Al-Karadaghi, S. / Liljas, A. ...Fedorov, R.V. / Meshcheryakov, V.A. / Gongadze, G.M. / Fomenkova, N.P. / Nevskaya, N.A. / Selmer, M. / Laurberg, M. / Kristensen, O. / Al-Karadaghi, S. / Liljas, A. / Garber, M.B. / Nikonov, S.V. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Structure of ribosomal protein TL5 complexed with RNA provides new insights into the CTC family of stress proteins. Authors: Fedorov, R. / Meshcheryakov, V. / Gongadze, G. / Fomenkova, N. / Nevskaya, N. / Selmer, M. / Laurberg, M. / Kristensen, O. / Al-Karadaghi, S. / Liljas, A. / Garber, M. / Nikonov, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1feu.cif.gz | 144.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1feu.ent.gz | 108.4 KB | Display | PDB format |
PDBx/mmJSON format | 1feu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1feu_validation.pdf.gz | 479.9 KB | Display | wwPDB validaton report |
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Full document | 1feu_full_validation.pdf.gz | 491.7 KB | Display | |
Data in XML | 1feu_validation.xml.gz | 22.5 KB | Display | |
Data in CIF | 1feu_validation.cif.gz | 33.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fe/1feu ftp://data.pdbj.org/pub/pdb/validation_reports/fe/1feu | HTTPS FTP |
-Related structure data
Similar structure data |
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-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 , 2 types, 4 molecules BECF
#1: RNA chain | Mass: 6206.706 Da / Num. of mol.: 2 / Fragment: INCLUDES LOOP E AND HELIX IV / Source method: obtained synthetically #2: RNA chain | Mass: 6790.141 Da / Num. of mol.: 2 / Fragment: INCLUDES LOOP E AND HELIX IV / Source method: obtained synthetically |
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-Protein , 1 types, 2 molecules AD
#3: Protein | Mass: 23252.600 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Description: BACTERIA / Production host: Escherichia coli (E. coli) / References: UniProt: P56930 |
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-Non-polymers , 3 types, 325 molecules
#4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-CD / #6: 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: 3.31 Å3/Da / Density % sol: 62.79 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.3→20 Å / Num. all: 41886 / Num. obs: 41886 / % possible obs: 98.8 % / Observed criterion σ(F): 6 / Observed criterion σ(I): 3 / Redundancy: 5.6 % / Biso Wilson estimate: 44.14 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 17 | |||||||||||||||
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.365 / Num. unique all: 2067 / % possible all: 97.8 | |||||||||||||||
Reflection | *PLUS Num. measured all: 188440 | |||||||||||||||
Reflection shell | *PLUS % possible obs: 97.8 % / Mean I/σ(I) obs: 4.5 |
-Processing
Software |
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Refinement | Resolution: 2.3→8 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.3→8 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.208 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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