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Yorodumi- PDB-3qui: Crystal structure of Pseudomonas aeruginosa Hfq in complex with ADPNP -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qui | ||||||
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Title | Crystal structure of Pseudomonas aeruginosa Hfq in complex with ADPNP | ||||||
Components | Protein hfq | ||||||
Keywords | RNA BINDING PROTEIN / LSM / RNA-binding protein / sRNA / mRNA / RNA CHAPERONE | ||||||
Function / homology | Function and homology information regulation of carbon utilization / regulation of translation, ncRNA-mediated / regulation of RNA stability / quorum sensing / regulation of translation / regulation of DNA-templated transcription / RNA binding / cytosol Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.933 Å | ||||||
Authors | Nikulin, A.D. / Murina, V.N. / Gabdulkhakov, A.G. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: Hfq binds ribonucleotides in three different RNA-binding sites. Authors: Murina, V. / Lekontseva, N. / Nikulin, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qui.cif.gz | 103.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qui.ent.gz | 79.9 KB | Display | PDB format |
PDBx/mmJSON format | 3qui.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qu/3qui ftp://data.pdbj.org/pub/pdb/validation_reports/qu/3qui | HTTPS FTP |
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-Related structure data
Related structure data | 4j5yC 4j6wC 4j6xC 4j6yC 1u1tS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 9114.487 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: hfq, PA4944 / Plasmid: PET22B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HUM0 |
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-Non-polymers , 5 types, 218 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PEG / | #5: Chemical | ChemComp-ADE / | #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: 1.98 Å3/Da / Density % sol: 37.86 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 200 mM ammonium sulphate, 200 mM NaCl, 50 mM Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 9, 2010 |
Radiation | Monochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. all: 29725 / Num. obs: 29725 / % possible obs: 89.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.95→2.04 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 1.97 / Num. unique all: 3127 / % possible all: 66.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1U1T Resolution: 1.933→47.577 Å / SU ML: 0.25 / Isotropic thermal model: OVERALL ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.774 Å2 / ksol: 0.38 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.933→47.577 Å
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Refine LS restraints |
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LS refinement shell |
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