+Open data
-Basic information
Entry | Database: PDB / ID: 4mmk | ||||||
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Title | Q8A Hfq from Pseudomonas aeruginosa | ||||||
Components | Protein hfq | ||||||
Keywords | RNA BINDING PROTEIN / LSM fold | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.156 Å | ||||||
Authors | Murina, V.N. / Filimonov, V.V. / Melnik, B.S. / Uhlein, M. / Mueller, U. / Weiss, M. / Nikulin, A.D. | ||||||
Citation | Journal: Biochemistry Mosc. / Year: 2014 Title: Effect of conserved intersubunit amino Acid substitutions on hfq protein structure and stability. Authors: Murina, V.N. / Melnik, B.S. / Filimonov, V.V. / Uhlein, M. / Weiss, M.S. / Muller, U. / 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 | 4mmk.cif.gz | 181.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mmk.ent.gz | 145.7 KB | Display | PDB format |
PDBx/mmJSON format | 4mmk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4mmk_validation.pdf.gz | 550.8 KB | Display | wwPDB validaton report |
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Full document | 4mmk_full_validation.pdf.gz | 571.5 KB | Display | |
Data in XML | 4mmk_validation.xml.gz | 35.5 KB | Display | |
Data in CIF | 4mmk_validation.cif.gz | 51.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mm/4mmk ftp://data.pdbj.org/pub/pdb/validation_reports/mm/4mmk | HTTPS FTP |
-Related structure data
Related structure data | 4mmlC 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 12 molecules ABCDEFGHIJKL
#1: Protein | Mass: 9057.437 Da / Num. of mol.: 12 / Mutation: Q8A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: hfq, PA4944 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HUM0 |
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-Non-polymers , 5 types, 353 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-K / #4: Chemical | #5: Chemical | ChemComp-SO4 / | #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: 2.06 Å3/Da / Density % sol: 40.29 % |
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Crystal grow | Temperature: 303 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 7% w/v PEG2000 MME, 2% MPD, 20 micromolar zinc chloride, 50 mM Tris-HCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 303.0K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Apr 30, 2010 / Details: Helios mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.156→35 Å / Num. all: 45536 / Num. obs: 45536 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.96 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.0886 / Rsym value: 0.0814 / Net I/σ(I): 10.68 |
Reflection shell | Resolution: 2.156→2.25 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 2.64 / Rsym value: 0.377 / % possible all: 75.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1U1S Resolution: 2.156→33.311 Å / Isotropic thermal model: ISOTROPIC / σ(F): 0 / Phase error: 38.87 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.48 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.156→33.311 Å
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Refine LS restraints |
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LS refinement shell |
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