+Open data
-Basic information
Entry | Database: PDB / ID: 1dmg | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF RIBOSOMAL PROTEIN L4 | ||||||
Components | RIBOSOMAL PROTEIN L4 | ||||||
Keywords | GENE REGULATION / ALPHA-BETA / RIBOSOMAL PROTEIN / L4 / RIBOSOME / RNA / S10 OPERON | ||||||
Function / homology | Function and homology information rRNA binding / ribosome / structural constituent of ribosome / translation Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å | ||||||
Authors | Worbs, M. / Huber, R. / Wahl, M.C. | ||||||
Citation | Journal: EMBO J. / Year: 2000 Title: Crystal structure of ribosomal protein L4 shows RNA-binding sites for ribosome incorporation and feedback control of the S10 operon. Authors: Worbs, M. / Huber, R. / Wahl, M.C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1dmg.cif.gz | 53.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1dmg.ent.gz | 37.9 KB | Display | PDB format |
PDBx/mmJSON format | 1dmg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dmg_validation.pdf.gz | 387 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1dmg_full_validation.pdf.gz | 388.9 KB | Display | |
Data in XML | 1dmg_validation.xml.gz | 5.3 KB | Display | |
Data in CIF | 1dmg_validation.cif.gz | 8.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dm/1dmg ftp://data.pdbj.org/pub/pdb/validation_reports/dm/1dmg | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 25690.898 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Plasmid: PET22B+ / Production host: Escherichia coli (E. coli) / References: UniProt: P38516 |
---|---|
#2: Chemical | ChemComp-CIT / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 45.97 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 3.8 Details: PEG400, AMMONIUM ACETATE, CITRATE, pH 3.8, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 7 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.07 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 3, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→15 Å / Num. all: 25013 / Num. obs: 23468 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 23.8 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 25.9 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 2 % / Rmerge(I) obs: 0.32 / % possible all: 88 |
Reflection shell | *PLUS % possible obs: 88 % / Mean I/σ(I) obs: 3.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.7→8 Å / σ(F): 2 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|