+Open data
-Basic information
Entry | Database: PDB / ID: 5i21 | |||||||||
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Title | Y55W Hfq from Pseudomonas aeruginosa | |||||||||
Components | RNA-binding protein Hfq | |||||||||
Keywords | RNA BINDING PROTEIN / Hfq / Pseudomonas aeruginosa | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Pseudomonas aeruginosa (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | |||||||||
Authors | Nikulin, A.D. / Lekontseva, N.V. | |||||||||
Funding support | Russian Federation, 1items
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Citation | Journal: To Be Published Title: Y55W Hfq from Pseudomonas aeruginosa Authors: Nikulin, A.D. / Lekontseva, N.V. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5i21.cif.gz | 57.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5i21.ent.gz | 41.4 KB | Display | PDB format |
PDBx/mmJSON format | 5i21.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i2/5i21 ftp://data.pdbj.org/pub/pdb/validation_reports/i2/5i21 | HTTPS FTP |
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-Related structure data
Related structure data | 1u1sS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 9137.524 Da / Num. of mol.: 3 / Mutation: Y55W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain PA7) (bacteria) Gene: hfq, PSPA7_5673 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A6VD57 #2: Chemical | ChemComp-CL / | #3: 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: 1.95 Å3/Da / Density % sol: 36.98 % |
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Crystal grow | Temperature: 303 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 7% W/V PEG2000 MME, 2% MPD, 50 MM TRIS-HCL, PH 6.5, |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.86 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 5, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.86 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→40 Å / Num. obs: 31293 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Biso Wilson estimate: 16.57 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.04633 / Net I/σ(I): 25.89 |
Reflection shell | Resolution: 1.55→1.65 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.5224 / Mean I/σ(I) obs: 4.09 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1U1S Resolution: 1.55→37.434 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.87
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→37.434 Å
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Refine LS restraints |
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LS refinement shell |
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