+Open data
-Basic information
Entry | Database: PDB / ID: 1lou | ||||||
---|---|---|---|---|---|---|---|
Title | RIBOSOMAL PROTEIN S6 | ||||||
Components | RIBOSOMAL PROTEIN S6 | ||||||
Keywords | RIBOSOME / PROTEIN FOLDING / TWO-STATE MODEL / TRANSITION STATE / REACTION COORDINATE / PROTEIN ENGINEERING | ||||||
Function / homology | Function and homology information small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / structural constituent of ribosome / translation Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Otzen, D.E. / Kristensen, O. / Proctor, M. / Oliveberg, M. | ||||||
Citation | Journal: Biochemistry / Year: 1999 Title: Structural changes in the transition state of protein folding: alternative interpretations of curved chevron plots. Authors: Otzen, D.E. / Kristensen, O. / Proctor, M. / Oliveberg, M. #1: Journal: Biochemistry / Year: 1997 Title: High-Energy Channelling in Protein Folding Authors: Silow, M. / Oliveberg, M. #2: Journal: Embo J. / Year: 1994 Title: Crystal Structure of the Ribosomal Protein S6 from Thermus Thermophilus Authors: Lindahl, M. / Svensson, L.A. / Liljas, A. / Sedelnikova, S.E. / Eliseikina, I.A. / Fomenkova, N.P. / Nevskaya, N. / Nikonov, S.V. / Garber, M.B. / Muranova, T.A. / Rykonova, A.I. / Amons, R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1lou.cif.gz | 32.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1lou.ent.gz | 21.8 KB | Display | PDB format |
PDBx/mmJSON format | 1lou.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lou_validation.pdf.gz | 426.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1lou_full_validation.pdf.gz | 427.8 KB | Display | |
Data in XML | 1lou_validation.xml.gz | 6.8 KB | Display | |
Data in CIF | 1lou_validation.cif.gz | 8.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lo/1lou ftp://data.pdbj.org/pub/pdb/validation_reports/lo/1lou | HTTPS FTP |
-Related structure data
Related structure data | 1risS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 11946.673 Da / Num. of mol.: 1 / Mutation: L30A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P23370 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 44 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 7.5 / Details: pH 7.5 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 287 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 23, 1998 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→52.9 Å / Num. obs: 8414 / % possible obs: 96.4 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 17.5 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 18 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 4.4 % / Rsym value: 0.314 / % possible all: 94.2 |
Reflection | *PLUS Num. measured all: 62306 |
Reflection shell | *PLUS Rmerge(I) obs: 0.314 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RIS Resolution: 1.95→20 Å / SU B: 3.54 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.18 / ESU R Free: 0.17
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.191 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|