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- PDB-1i4k: CRYSTAL STRUCTURE OF AN SM-LIKE PROTEIN (AF-SM1) FROM ARCHAEOGLOB... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1i4k | ||||||
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Title | CRYSTAL STRUCTURE OF AN SM-LIKE PROTEIN (AF-SM1) FROM ARCHAEOGLOBUS FULGIDUS AT 2.5A RESOLUTION | ||||||
![]() | PUTATIVE SNRNP SM-LIKE PROTEIN | ||||||
![]() | RNA BINDING PROTEIN / SNRNP / SM / CORE SNRNP DOMAIN | ||||||
Function / homology | ![]() Lsm1-7-Pat1 complex / intracellular organelle / ribonucleoprotein complex / RNA binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Toro, I. / Thore, S. / Mayer, C. / Basquin, J. / Seraphin, B. / Suck, D. | ||||||
![]() | ![]() Title: RNA binding in an Sm core domain: X-ray structure and functional analysis of an archaeal Sm protein complex. Authors: Toro, I. / Thore, S. / Mayer, C. / Basquin, J. / Seraphin, B. / Suck, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 367.8 KB | Display | ![]() |
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PDB format | ![]() | 308.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 673.1 KB | Display | ![]() |
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Full document | ![]() | 750.4 KB | Display | |
Data in XML | ![]() | 76 KB | Display | |
Data in CIF | ![]() | 104.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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5 | ![]()
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6 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 8391.709 Da / Num. of mol.: 28 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.46 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.3 Details: PEG 6000, sodium citrate, pH 4.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 14, 2000 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.842 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. all: 63291 / Num. obs: 63291 / % possible obs: 99.3 % / Redundancy: 4.04 % / Biso Wilson estimate: 46.889 Å2 / Rsym value: 0.072 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 3.34 % / Mean I/σ(I) obs: 3.5 / Num. unique all: 6999 / Rsym value: 0.353 / % possible all: 99.9 |
Reflection | *PLUS Num. measured all: 255898 / Rmerge(I) obs: 0.072 |
Reflection shell | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 2.6 Å / % possible obs: 99.9 % / Rmerge(I) obs: 0.353 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: A seven membered ring of an Sm-like protein from Pyrococcus abyssii. Resolution: 2.5→20 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 59.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor obs: 0.207 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 59.6 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.5 Å / Rfactor Rfree: 0.333 / % reflection Rfree: 5 % / Rfactor Rwork: 0.28 |