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Yorodumi- PDB-4x9d: High-resolution structure of Hfq from Methanococcus jannaschii in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4x9d | ||||||
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Title | High-resolution structure of Hfq from Methanococcus jannaschii in complex with UMP | ||||||
Components | Uncharacterized protein MJ1435 | ||||||
Keywords | RNA BINDING PROTEIN / Hfq / archaeal Lsm | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Nikulin, A.D. / Tishchenko, S.V. / Nikonova, E.Y. / Murina, V.N. / Mihailina, A.O. / Lekontseva, N.V. | ||||||
Funding support | Russian Federation, 1items
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Citation | Journal: J. Biomol. Struct. Dyn. / Year: 2017 Title: Characterization of RNA-binding properties of the archaeal Hfq-like protein from Methanococcus jannaschii. Authors: Nikulin, A. / Mikhailina, A. / Lekontseva, N. / Balobanov, V. / Nikonova, E. / Tishchenko, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4x9d.cif.gz | 98.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4x9d.ent.gz | 74.6 KB | Display | PDB format |
PDBx/mmJSON format | 4x9d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x9/4x9d ftp://data.pdbj.org/pub/pdb/validation_reports/x9/4x9d | HTTPS FTP |
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-Related structure data
Related structure data | 4x9cSC 5dy9C 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
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 8309.771 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Gene: MJ1435 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q58830 |
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-Non-polymers , 9 types, 262 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-NA / #5: Chemical | ChemComp-U5P / #6: Chemical | ChemComp-EDO / | #7: Chemical | #8: Chemical | #9: Chemical | ChemComp-PEG / | #10: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.88 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8 Details: A2 JBCScreen Nuc-Pro 1 (50% PEG200, 0,1M Tris-HCl, pH 8,0) in presence of 25 mM UMP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.86 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 5, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.86 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. all: 68667 / Num. obs: 68667 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.0726 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.3 / % possible all: 95.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4X9C Resolution: 1.5→43.704 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.74 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→43.704 Å
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Refine LS restraints |
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LS refinement shell |
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