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Yorodumi- PDB-4gfq: 2.65 Angstrom Resolution Crystal Structure of Ribosome Recycling ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4gfq | ||||||
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Title | 2.65 Angstrom Resolution Crystal Structure of Ribosome Recycling Factor (frr) from Bacillus anthracis | ||||||
Components | Ribosome-recycling factor | ||||||
Keywords | TRANSLATION / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus anthracis (anthrax bacterium) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Minasov, G. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: TO BE PUBLISHED Title: 2.65 Angstrom Resolution Crystal Structure of Ribosome Recycling Factor (frr) from Bacillus anthracis Authors: Minasov, G. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gfq.cif.gz | 90.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gfq.ent.gz | 69.6 KB | Display | PDB format |
PDBx/mmJSON format | 4gfq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gf/4gfq ftp://data.pdbj.org/pub/pdb/validation_reports/gf/4gfq | HTTPS FTP |
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-Related structure data
Related structure data | 1ek8S 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 23455.588 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Sterne / Gene: BAS3675, BA_3962, frr, GBAA_3962 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic / References: UniProt: Q81WL1 |
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-Non-polymers , 5 types, 32 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PO4 / | #5: Chemical | ChemComp-PEG / | #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: 3.1 Å3/Da / Density % sol: 60.31 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 Details: protein: 7.4 mg/mL in 0.25 M sodium cloride, 0.01 M Tris-HCl, pH 8.3, screen: Classics II (H3), 0.24 M sodium malonate, pH 7.0, 20% w/v PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.07806 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 4, 2012 / Details: mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07806 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→30 Å / Num. all: 8662 / Num. obs: 8662 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 87.2 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 18 |
Reflection shell | Resolution: 2.65→2.7 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 2.5 / Num. unique all: 430 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EK8 Resolution: 2.65→28.81 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / SU B: 26.974 / SU ML: 0.249 Isotropic thermal model: THERMAL FACTORS INDIVIDUALLY REFINED Cross valid method: THROUGHOUT / ESU R: 0.563 / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 66.329 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→28.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.65→2.718 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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