+Open data
-Basic information
Entry | Database: PDB / ID: 2qvw | ||||||
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Title | Structure of Giardia Dicer refined against twinned data | ||||||
Components | GLP_546_48378_50642 | ||||||
Keywords | HYDROLASE / Dicer / RNAi / pseudo-merohedral twin | ||||||
Function / homology | Function and homology information apoptotic DNA fragmentation / deoxyribonuclease I activity / ribonuclease III activity / pre-miRNA processing / siRNA processing / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / RISC complex / nucleotide binding / RNA binding / nucleus ...apoptotic DNA fragmentation / deoxyribonuclease I activity / ribonuclease III activity / pre-miRNA processing / siRNA processing / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / RISC complex / nucleotide binding / RNA binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Giardia intestinalis (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å | ||||||
Authors | Doudna, J.A. / MacRae, I.J. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2007 Title: An unusual case of pseudo-merohedral twinning in orthorhombic crystals of Dicer Authors: Macrae, I.J. / Doudna, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qvw.cif.gz | 540.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qvw.ent.gz | 444.9 KB | Display | PDB format |
PDBx/mmJSON format | 2qvw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2qvw_validation.pdf.gz | 484.2 KB | Display | wwPDB validaton report |
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Full document | 2qvw_full_validation.pdf.gz | 643.5 KB | Display | |
Data in XML | 2qvw_validation.xml.gz | 114.2 KB | Display | |
Data in CIF | 2qvw_validation.cif.gz | 153.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qv/2qvw ftp://data.pdbj.org/pub/pdb/validation_reports/qv/2qvw | HTTPS FTP |
-Related structure data
Related structure data | 2fflS 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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3 |
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4 |
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Unit cell |
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Details | The biological unit is a monomer. There are four copies in the asymmetric unit. |
-Components
#1: Protein | Mass: 82690.070 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Giardia intestinalis (eukaryote) / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q7R2M2, UniProt: A8BQJ3*PLUS, ribonuclease III #2: Chemical | ChemComp-MN / |
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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: 3.17 Å3/Da / Density % sol: 61.17 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 28% PEG 400, 0.1M NaCl, 0.1M MgCl2, 0.1M MES, 5 mM TCEP, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 5, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection twin | Type: hemihedral / Operator: l,-k,h / Fraction: 0.5 |
Reflection | Resolution: 3→50 Å / Num. all: 84015 / Num. obs: 82755 / % possible obs: 98.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 3 / Redundancy: 5.7 % / Biso Wilson estimate: 68.7 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 20.9 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 4.21 / Num. unique all: 8238 / Rsym value: 0.371 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Starting model: PDB entry 2FFL Resolution: 3→50 Å / σ(F): 1517 Details: The authors state that the structure is the same as the previously deposited Dicer structure (PDB entry 2FFL) except the new model has been refined against higher resolution, twinned data.
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Solvent computation | Bsol: 21.105 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.525 Å2
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Refinement step | Cycle: LAST / Resolution: 3→50 Å
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Refine LS restraints |
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Xplor file |
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