+Open data
-Basic information
Entry | Database: PDB / ID: 6tfl | ||||||
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Title | Lsm protein (SmAP) from Halobacterium salinarum | ||||||
Components | RNA-binding protein Lsm | ||||||
Keywords | RNA BINDING PROTEIN / Lsm / SmAP / RNA-chaperon | ||||||
Function / homology | LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / LSM domain superfamily / URIDINE / RNA-binding protein Lsm Function and homology information | ||||||
Biological species | Halobacterium salinarum R1 (Halophile) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.397 Å | ||||||
Authors | Nikulin, A.D. / Fando, M.S. / Lekontseva, N.V. | ||||||
Funding support | Russian Federation, 1items
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Citation | Journal: Biochemistry Mosc. / Year: 2021 Title: Structure and RNA-Binding Properties of Lsm Protein from Halobacterium salinarum. Authors: Fando, M.S. / Mikhaylina, A.O. / Lekontseva, N.V. / Tishchenko, S.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 | 6tfl.cif.gz | 192.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tfl.ent.gz | 153.7 KB | Display | PDB format |
PDBx/mmJSON format | 6tfl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tfl_validation.pdf.gz | 472.7 KB | Display | wwPDB validaton report |
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Full document | 6tfl_full_validation.pdf.gz | 479.2 KB | Display | |
Data in XML | 6tfl_validation.xml.gz | 16.9 KB | Display | |
Data in CIF | 6tfl_validation.cif.gz | 29.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tf/6tfl ftp://data.pdbj.org/pub/pdb/validation_reports/tf/6tfl | HTTPS FTP |
-Related structure data
Related structure data | 1ljoS S: Starting model for refinement |
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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
#1: Protein | Mass: 6767.518 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Details: This protein has two additional amino acid residues at the N-terminus because of TEV protease specificity. Source: (gene. exp.) Halobacterium salinarum R1 (Halophile) / Gene: lsm, snp, OE_3142R / Production host: Escherichia coli (E. coli) / References: UniProt: B0R5R2 #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-URI / #4: Chemical | ChemComp-GOL / | #5: 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 | Density Matthews: 3.44 Å3/Da / Density % sol: 64.28 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 15% PEG 8000; 100mM MES pH=6.5; 200mM calcium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 2, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9724 Å / Relative weight: 1 |
Reflection | Resolution: 2.397→50 Å / Num. obs: 1318697 / % possible obs: 99.75 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 19.9 % / Biso Wilson estimate: 42.7 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.261 / Rpim(I) all: 0.069 / Rrim(I) all: 0.061 / Χ2: 1.36 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2.397→2.483 Å / Redundancy: 15 % / Rmerge(I) obs: 0.908 / Mean I/σ(I) obs: 2.34 / Num. unique obs: 82803 / CC1/2: 0.891 / Rpim(I) all: 0.232 / Rrim(I) all: 0.937 / Χ2: 1.11 / % possible all: 98.38 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1LJO Resolution: 2.397→50 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.74
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 108.34 Å2 / Biso mean: 47.4693 Å2 / Biso min: 26 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.397→50 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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