+Open data
-Basic information
Entry | Database: PDB / ID: 8p9m | ||||||
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Title | Hexameric Hfq from Chromobacterium haemolyticum | ||||||
Components | RNA-binding protein Hfq | ||||||
Keywords | RNA BINDING PROTEIN / Hfq / RNA-chaperon | ||||||
Function / homology | RNA-binding protein Hfq / Hfq protein / : / Sm domain profile. / LSM domain superfamily / regulation of DNA-templated transcription / RNA binding / RNA-binding protein Hfq Function and homology information | ||||||
Biological species | Chromobacterium haemolyticum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Nikulin, A.D. / Lekontseva, N.V. | ||||||
Funding support | Russian Federation, 1items
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Citation | Journal: Crystallography Reports / Year: 2023 Title: The Structure of the Hfq Protein from Chromobacterium haemolyticum Revealed a New Variant of Regulation of RNA Binding with the Protein Authors: Lekontseva, N.V. / Nikulin, A.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8p9m.cif.gz | 98.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8p9m.ent.gz | 75.2 KB | Display | PDB format |
PDBx/mmJSON format | 8p9m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8p9m_validation.pdf.gz | 483.6 KB | Display | wwPDB validaton report |
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Full document | 8p9m_full_validation.pdf.gz | 489.6 KB | Display | |
Data in XML | 8p9m_validation.xml.gz | 19 KB | Display | |
Data in CIF | 8p9m_validation.cif.gz | 27.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p9/8p9m ftp://data.pdbj.org/pub/pdb/validation_reports/p9/8p9m | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 9690.183 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chromobacterium haemolyticum (bacteria) Gene: hfq, B0T39_13335, B0T45_12055, CH06BL_33310, DBB33_18715 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1W0CX06 #2: Chemical | ChemComp-GOL / | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 15% PEG4000, 50 mM Tris-HCl, pH 7.5, 150 mM KCl, 20 mM MgCl2 |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU PhotonJet-R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Nov 30, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→22.33 Å / Num. obs: 27718 / % possible obs: 98.38 % / Redundancy: 1.9 % / Biso Wilson estimate: 27.49 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.068 / Rrim(I) all: 0.096 / Net I/σ(I): 8.19 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 0.92 / Num. unique obs: 5300 / CC1/2: 0.579 / Rpim(I) all: 0.76 / Rrim(I) all: 1.07 / % possible all: 99.71 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→22.33 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.91 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→22.33 Å
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Refine LS restraints |
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LS refinement shell |
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