+Open data
-Basic information
Entry | Database: PDB / ID: 4jhj | ||||||
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Title | Crystal structure of Danio rerio Slip1 in complex with Dbp5 | ||||||
Components |
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Keywords | TRANSLATION / DEAD-BOX HELICASE / MRNA EXPORT / RECA-LIKE / RNA-DEPENDENT ATPASE / DDX19 / DEAD-BOX PROTEIN 19B / MRNA TRANSPORT / ATP BINDING / HELICASE / HYDROLASE / NUCLEOTIDE BINDING / RNA BINDING / TRANSPORT HISTONE MRNA PROCESSING / 3'-UTR / 3'-PROCESSING / NUP214 | ||||||
Function / homology | Function and homology information histone mRNA stem-loop binding complex / cap-dependent translational initiation / translation activator activity / regulation of translational initiation / poly(A)+ mRNA export from nucleus / cytoplasmic stress granule / RNA helicase activity / RNA helicase / RNA binding / ATP binding ...histone mRNA stem-loop binding complex / cap-dependent translational initiation / translation activator activity / regulation of translational initiation / poly(A)+ mRNA export from nucleus / cytoplasmic stress granule / RNA helicase activity / RNA helicase / RNA binding / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Danio rerio (zebrafish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å | ||||||
Authors | Von Moeller, H. / Conti, E. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2013 Title: Structural and biochemical studies of SLIP1-SLBP identify DBP5 and eIF3g as SLIP1-binding proteins. Authors: von Moeller, H. / Lerner, R. / Ricciardi, A. / Basquin, C. / Marzluff, W.F. / Conti, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jhj.cif.gz | 102 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jhj.ent.gz | 79.2 KB | Display | PDB format |
PDBx/mmJSON format | 4jhj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jh/4jhj ftp://data.pdbj.org/pub/pdb/validation_reports/jh/4jhj | HTTPS FTP |
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-Related structure data
Related structure data | 4jhkC 2i2oS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 6
NCS ensembles :
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-Components
#1: Protein | Mass: 25794.500 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-222 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: mif4gdb, zgc:110826 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q5EAQ1 #2: Protein/peptide | Mass: 3495.730 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-32 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: ddx19 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: Q7ZU28, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides #3: Water | ChemComp-HOH / | |
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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: 4.73 Å3/Da / Density % sol: 73.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.05 M MES pH 6.0, 18% (w/v) PEG 8000, 0.2 M Ca-Acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 22, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 3.25→86.13 Å / Num. obs: 16724 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Rsym value: 0.083 / Net I/σ(I): 16.34 |
Reflection shell | Resolution: 3.25→3.45 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.68 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2I2O Resolution: 3.25→73.77 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.912 / SU B: 25.36 / SU ML: 0.403 / Cross valid method: THROUGHOUT / ESU R Free: 0.446 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 102.3 Å2
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Refinement step | Cycle: LAST / Resolution: 3.25→73.77 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 3.25→3.33 Å / Total num. of bins used: 20
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