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- PDB-2qtx: Crystal structure of an Hfq-like protein from Methanococcus jannaschii -
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Open data
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Basic information
Entry | Database: PDB / ID: 2qtx | ||||||
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Title | Crystal structure of an Hfq-like protein from Methanococcus jannaschii | ||||||
![]() | Uncharacterized protein MJ1435 | ||||||
![]() | RNA BINDING PROTEIN / Hfq / Sm / RNA-binding protein / sRNA / translational regulation | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Nielsen, J.S. / Boggild, A. / Andersen, C.B.F. / Nielsen, G. / Boysen, A. / Brodersen, D.E. / Valentin-Hansen, P. | ||||||
![]() | ![]() Title: An Hfq-like protein in archaea: Crystal structure and functional characterization of the Sm protein from Methanococcus jannaschii. Authors: Nielsen, J.S. / Boggild, A. / Andersen, C.B. / Nielsen, G. / Boysen, A. / Brodersen, D.E. / Valentin-Hansen, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 287 KB | Display | ![]() |
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PDB format | ![]() | 235 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 504.7 KB | Display | ![]() |
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Full document | ![]() | 508.8 KB | Display | |
Data in XML | ![]() | 24.3 KB | Display | |
Data in CIF | ![]() | 35 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1u1sS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Details | The biological assembly is a homohexamer. The asu contains two hexamers. |
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Components
#1: Protein | Mass: 8309.771 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: pTYP11 / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.31 % |
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Crystal grow | Temperature: 277 K / pH: 8.5 Details: 25% PEG 3350, 0.2M Ammonium Acetate, 0.1M Tris, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 8.50 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 17, 2006 / Details: DYNAMICALLY BENDABLE MIRRORS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: FIXED EXIT SI 111 MONCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9993 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 3.4 % / Av σ(I) over netI: 17 / Number: 96326 / Rmerge(I) obs: 0.056 / Χ2: 1.5 / D res high: 2.5 Å / D res low: 250 Å / Num. obs: 28424 / % possible obs: 92.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2.5→250 Å / Num. obs: 28424 / % possible obs: 92.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 48.18 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 17 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.209 / Mean I/σ(I) obs: 3.7 / % possible all: 57.5 |
-Phasing
Phasing | Method: ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||
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Phasing MR |
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Phasing dm | FOM : 0.62 / FOM acentric: 0.62 / FOM centric: 0.62 / Reflection: 28398 / Reflection acentric: 27025 / Reflection centric: 1373 | |||||||||||||||||||||||||||||||||||||||||||||||||
Phasing dm shell |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1U1S Resolution: 2.5→38.5 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 30.003 Å2 / ksol: 0.326 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.43 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→38.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.59 Å / Total num. of bins used: 54
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