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Yorodumi- PDB-1vmb: Crystal structure of 30S ribosomal protein S6 (TM0603) from Therm... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vmb | ||||||
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Title | Crystal structure of 30S ribosomal protein S6 (TM0603) from Thermotoga maritima at 1.70 A resolution | ||||||
Components | 30S ribosomal protein S6 | ||||||
Keywords | TRANSLATION / TM0603 / 30S RIBOSOMAL PROTEIN S6 / STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI / Joint Center for Structural Genomics | ||||||
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 | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of 30S ribosomal protein S6 (TM0603) from Thermotoga maritima at 1.70 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vmb.cif.gz | 40.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vmb.ent.gz | 26.8 KB | Display | PDB format |
PDBx/mmJSON format | 1vmb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1vmb_validation.pdf.gz | 438.1 KB | Display | wwPDB validaton report |
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Full document | 1vmb_full_validation.pdf.gz | 438.3 KB | Display | |
Data in XML | 1vmb_validation.xml.gz | 7.8 KB | Display | |
Data in CIF | 1vmb_validation.cif.gz | 10.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vm/1vmb ftp://data.pdbj.org/pub/pdb/validation_reports/vm/1vmb | HTTPS FTP |
-Related structure data
Related structure data | 1louS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 16857.137 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: rpsF,TM0603 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WZ72 | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 47.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop, nanodrop Details: 20.0% PEG-3350, 0.1M NaAcetate, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.980075 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 24, 2004 / Details: flat mirror |
Radiation | Monochromator: single crystal Si(311) bent monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.980075 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→47.62 Å / Num. obs: 15840 / % possible obs: 96.2 % / Redundancy: 5.4 % / Biso Wilson estimate: 29.25 Å2 / Rsym value: 0.073 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 1.7→1.74 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 880 / Rsym value: 0.391 / % possible all: 73.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1lou Resolution: 1.7→47.62 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.902 / SU B: 3.859 / SU ML: 0.067 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.517 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→47.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 25.2294 Å / Origin y: 7.889 Å / Origin z: 32.502 Å
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Refinement TLS group | Selection: ALL |