+Open data
-Basic information
Entry | Database: PDB / ID: 3inz | ||||||
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Title | H57T Hfq from Pseudomonas aeruginosa | ||||||
Components | Protein hfq | ||||||
Keywords | RNA BINDING PROTEIN / Hfq / protein tertiary structure / RNA-binding / Stress response / RNA-BINDING PROTEIN | ||||||
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: 1.7 Å | ||||||
Authors | Moskaleva, O. / Melnik, B. / Gabdulkhakov, A. / Garber, M. / Nikonov, S. / Stolboushkina, E. / Nikulin, A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2010 Title: The structures of mutant forms of Hfq from Pseudomonas aeruginosa reveal the importance of the conserved His57 for the protein hexamer organization. Authors: Moskaleva, O. / Melnik, B. / Gabdulkhakov, A. / Garber, M. / Nikonov, S. / Stolboushkina, E. / Nikulin, A. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2005 Title: Structure of Pseudomonas aeruginosa Hfq protein. Authors: Nikulin, A. / Stolboushkina, E. / Perederina, A. / Vassilieva, I. / Blaesi, U. / Moll, I. / Kachalova, G. / Yokoyama, S. / Vassylyev, D. / Garber, M. / Nikonov, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3inz.cif.gz | 197.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3inz.ent.gz | 158.1 KB | Display | PDB format |
PDBx/mmJSON format | 3inz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3inz_validation.pdf.gz | 476.4 KB | Display | wwPDB validaton report |
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Full document | 3inz_full_validation.pdf.gz | 488 KB | Display | |
Data in XML | 3inz_validation.xml.gz | 22.4 KB | Display | |
Data in CIF | 3inz_validation.cif.gz | 32.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/in/3inz ftp://data.pdbj.org/pub/pdb/validation_reports/in/3inz | HTTPS FTP |
-Related structure data
Related structure data | 3m4gC 1u1sS 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
#1: Protein | Mass: 9077.444 Da / Num. of mol.: 6 / Mutation: H57T 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 #2: Chemical | ChemComp-CD / #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-CL / | #5: 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: 2.09 Å3/Da / Density % sol: 41.15 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 8.5 Details: 4 mg/ml protein, 50 mM NaCl, 100 mM NH4Cl, 7,5% MMEPEG 2000, 50 mM Tris HCl, 10 mM CdCl2, pH 8.5, VAPOR DIFFUSION, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 26, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. obs: 50597 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 31.2 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 27.9 |
Reflection shell | Resolution: 1.7→1.74 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 3.9 / Num. unique all: 2983 / % possible all: 80.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1U1S Resolution: 1.7→30 Å / SU ML: 0.03 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 1.99 / Stereochemistry target values: Engh & Huber
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.003 Å2 / ksol: 0.384 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 1.1587 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→30 Å
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Refine LS restraints |
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LS refinement shell |
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