+Open data
-Basic information
Entry | Database: PDB / ID: 2ylc | ||||||
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Title | Structure of Salmonella typhimurium Hfq in complex with U6 RNA | ||||||
Components | PROTEIN HFQ | ||||||
Keywords | RNA BINDING PROTEIN / RNA-BINDING PROTEIN / LSM PROTEIN / RNA CHAPERONE | ||||||
Function / homology | Function and homology information regulation of translation, ncRNA-mediated / regulation of RNA stability / regulation of DNA-templated transcription / RNA binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Sauer, E. / Weichenrieder, O. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 Title: Structural Basis for RNA 3' End Recognition by Hfq Authors: Sauer, E. / Weichenrieder, O. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ylc.cif.gz | 56.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ylc.ent.gz | 41.2 KB | Display | PDB format |
PDBx/mmJSON format | 2ylc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yl/2ylc ftp://data.pdbj.org/pub/pdb/validation_reports/yl/2ylc | HTTPS FTP |
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-Related structure data
Related structure data | 2ylbSC 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: 8257.572 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-72 Source method: isolated from a genetically manipulated source Details: THE SEQUENCE IS PRECEDED BY A GA TAG REMAINING FROM THE PURIFICATION TAG. Source: (gene. exp.) SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria) Strain: LT2 / Plasmid: PET M60 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)GOLD / References: UniProt: P0A1R0 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-U / | #4: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE IS PRECEDED BY A GA TAG REMAINING FROM THE PURIFICATI | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 40 % / Description: NONE |
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Crystal grow | pH: 8 / Details: 0.2 M NASCN, 20% PEG3350, pH 8.0 |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.979 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 23, 2010 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→30.6 Å / Num. obs: 15112 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 9.1 % / Biso Wilson estimate: 13.31 Å2 / Rsym value: 0.077 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 1.3→1.4 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 3.6 / Rsym value: 0.69 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2YLB Resolution: 1.3→30.595 Å / SU ML: 0.14 / σ(F): 1.99 / Phase error: 18.33 / Stereochemistry target values: ML Details: HYDROGENS WERE REFINED IN THE RIDING POSITIONS. B FACTORS WERE REFINED ANISOTROPICALLY FOR NON-HYDROGEN ATOMS. THE FOLLOWING RESIDUES WERE MODELED AS DOUBLE CONFORMATIONS. CHAIN A, RESIDUE ...Details: HYDROGENS WERE REFINED IN THE RIDING POSITIONS. B FACTORS WERE REFINED ANISOTROPICALLY FOR NON-HYDROGEN ATOMS. THE FOLLOWING RESIDUES WERE MODELED AS DOUBLE CONFORMATIONS. CHAIN A, RESIDUE 27. THE FOLLOWING RESIDUES ARE DISORDERED. CHAIN A, RESIDUES 1 TO 4, 71 TO 72. THE DENSITY FOR THE HEXAURIDINE RNA IS AVERAGED AROUND THE SIXFOLD AXIS. THE ASYMMETRIC UNIT CONTAINS ONLY ONE OF THE SIX URIDINES WITH A PHOSPHATE OCCUPANCY OF 5 OUT OF 6, AND WITH COVALENT BONDS TO ITS NUCLEOTIDE NEIGHBORS. THE BIOLOGICAL UNIT IS AN HFQ HEXAMER BOUND TO THE HEXAURIDINE RNA SUBSTRATE.
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Solvent computation | Shrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.967 Å2 / ksol: 0.447 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.4 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→30.595 Å
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Refine LS restraints |
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LS refinement shell |
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