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- PDB-1m8x: CRYSTAL STRUCTURE OF THE PUMILIO-HOMOLOGY DOMAIN FROM HUMAN PUMIL... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1m8x | ||||||
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Title | CRYSTAL STRUCTURE OF THE PUMILIO-HOMOLOGY DOMAIN FROM HUMAN PUMILIO1 IN COMPLEX WITH NRE1-14 RNA | ||||||
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![]() | RNA BINDING PROTEIN/RNA / Pumilio-homology domain / Puf domain / Nanos response element / RNA BINDING PROTEIN-RNA COMPLEX | ||||||
Function / homology | ![]() regulation of miRNA-mediated gene silencing / positive regulation of miRNA-mediated gene silencing / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Wang, X. / McLachlan, J. / Zamore, P.D. / Hall, T.M.T. | ||||||
![]() | ![]() Title: MODULAR RECOGNITION OF RNA BY A HUMAN PUMILIO-HOMOLOGY DOMAIN Authors: Wang, X. / McLachlan, J. / Zamore, P.D. / Hall, T.M.T. #1: ![]() Title: CRYSTAL STRUCTURE OF A PUMILIO HOMOLOGY DOMAIN Authors: Wang, X. / Zamore, P.D. / Hall, T.M.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 166.3 KB | Display | ![]() |
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PDB format | ![]() | 129.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1m8wC ![]() 1m8yC ![]() 1ib3 C: citing same article ( 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Details | Two biological units are contained in the asymmetric unit. |
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Components
#1: RNA chain | Mass: 2489.489 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: This sequence occurs naturally in Drosophila melanogaster | ||
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#2: RNA chain | Mass: 2183.323 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: This sequence occurs naturally in Drosophila melanogaster | ||
#3: Protein | Mass: 40364.523 Da / Num. of mol.: 2 / Fragment: Pumilio-homology domain, Residues 828-1176 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #4: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.28 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: PEG 3350, lithium sulfate, sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 7, 2001 |
Radiation | Monochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.2→500 Å / Num. all: 39467 / Num. obs: 39467 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 27.4 Å2 / Rsym value: 0.083 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 3718 / Rsym value: 0.343 / % possible all: 93.2 |
Reflection | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 500 Å / Rmerge(I) obs: 0.083 |
Reflection shell | *PLUS % possible obs: 93.2 % / Num. unique obs: 3718 / Rmerge(I) obs: 0.343 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1IB3 ![]() 1ib3 Resolution: 2.2→34.29 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 57.1577 Å2 / ksol: 0.318186 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.1 Å2
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Refine analyze | Luzzati coordinate error free: 0.38 Å / Luzzati sigma a free: 0.36 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→34.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.2 Å / % reflection Rfree: 6 % / Rfactor all![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.36 / Rfactor Rwork: 0.32 |