+Open data
-Basic information
Entry | Database: PDB / ID: 3hfo | ||||||
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Title | Crystal Structure of an Hfq protein from Synechocystis sp. | ||||||
Components | Ssr3341 protein | ||||||
Keywords | RNA BINDING PROTEIN / HFQ / SM / RNA-BINDING PROTEIN / SRNA / TRANSLATIONAL REGULATION | ||||||
Function / homology | SH3 type barrels. - #100 / LSM domain superfamily / SH3 type barrels. / Roll / Mainly Beta / Ssr3341 protein Function and homology information | ||||||
Biological species | Synechocystis sp. PCC 6803 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å | ||||||
Authors | Boggild, A. / Overgaard, M. / Valentin-Hansen, P. / Brodersen, D.E. | ||||||
Citation | Journal: Febs J. / Year: 2009 Title: Cyanobacteria contain a structural homologue of the Hfq protein with altered RNA-binding properties. Authors: Boggild, A. / Overgaard, M. / Valentin-Hansen, P. / Brodersen, D.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hfo.cif.gz | 104.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hfo.ent.gz | 81.1 KB | Display | PDB format |
PDBx/mmJSON format | 3hfo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3hfo_validation.pdf.gz | 441.3 KB | Display | wwPDB validaton report |
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Full document | 3hfo_full_validation.pdf.gz | 444.1 KB | Display | |
Data in XML | 3hfo_validation.xml.gz | 13 KB | Display | |
Data in CIF | 3hfo_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hf/3hfo ftp://data.pdbj.org/pub/pdb/validation_reports/hf/3hfo | HTTPS FTP |
-Related structure data
Related structure data | 3hfnC 1hk9S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 7839.961 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: codons optimised for E. coli expression / Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC6803 / Gene: ssr3341 / Plasmid: pTYP11 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: P74112 #2: 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: 1.92 Å3/Da / Density % sol: 36.09 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 60% Tacsimate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.9 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 19, 2008 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal monochromator, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.21→26.2 Å / Num. obs: 52709 / % possible obs: 96.5 % / Redundancy: 4.8 % / Biso Wilson estimate: 16.864 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 24.23 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 51.73
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1HK9 Resolution: 1.3→26.199 Å / Occupancy max: 1 / Occupancy min: 0.16 / FOM work R set: 0.891 / SU ML: 0.04 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.911 Å2 / ksol: 0.389 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 64.74 Å2 / Biso mean: 17.734 Å2 / Biso min: 5.63 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→26.199 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12
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