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Yorodumi- PDB-4d26: Crystal structure of the Bombyx mori Vasa helicase (E339Q) in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4d26 | ||||||
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Title | Crystal structure of the Bombyx mori Vasa helicase (E339Q) in complex with RNA,ADP and Pi | ||||||
Components |
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Keywords | HYDROLASE / PIRNA / AMPLIFIER COMPLEX / TRANSPOSON | ||||||
Function / homology | Function and homology information intracellular organelle / nucleic acid binding / RNA helicase activity / hydrolase activity / RNA helicase / ATP binding Similarity search - Function | ||||||
Biological species | BOMBYX MORI (domestic silkworm) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Spinelli, P. / Pillai, R.S. / Kadlec, J. / Cusack, S. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2014 Title: RNA Clamping by Vasa Assembles a Pirna Amplifier Complex on Transposon Transcripts. Authors: Xiol, J. / Spinelli, P. / Laussmann, M.A. / Homolka, D. / Yang, Z. / Cora, E. / Coute, Y. / Conn, S. / Kadlec, J. / Sachidanandam, R. / Kaksonen, M. / Cusack, S. / Ephrussi, A. / Pillai, R.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4d26.cif.gz | 191.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4d26.ent.gz | 149.1 KB | Display | PDB format |
PDBx/mmJSON format | 4d26.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d2/4d26 ftp://data.pdbj.org/pub/pdb/validation_reports/d2/4d26 | HTTPS FTP |
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-Related structure data
Related structure data | 4d25C 2db3S C: citing same article (ref.) 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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Unit cell |
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-Components
-Protein / RNA chain , 2 types, 2 molecules AD
#1: Protein | Mass: 48129.074 Da / Num. of mol.: 1 / Fragment: HELICASE, RESIDUES 135-564 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) BOMBYX MORI (domestic silkworm) / Cell line: BMN4 OVARIAN CELL CULTURE / Plasmid: PETM11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: O01378 |
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#2: RNA chain | Mass: 1876.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) BOMBYX MORI (domestic silkworm) |
-Non-polymers , 4 types, 93 molecules
#3: Chemical | ChemComp-ADP / |
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#4: Chemical | ChemComp-PO4 / |
#5: Chemical | ChemComp-MG / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 45 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: 0.1M HEPES, PH 7.5, 25% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 18, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.939 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→100 Å / Num. obs: 26616 / % possible obs: 99.4 % / Observed criterion σ(I): 2.4 / Redundancy: 4 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 4 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.4 / % possible all: 95.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2DB3 Resolution: 2.1→43.78 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.901 / SU B: 9.952 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.049 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→43.78 Å
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Refine LS restraints |
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