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Yorodumi- PDB-1r6z: The Crystal Structure of the Argonaute2 PAZ domain (as a MBP fusion) -
+Open data
-Basic information
Entry | Database: PDB / ID: 1r6z | |||||||||
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Title | The Crystal Structure of the Argonaute2 PAZ domain (as a MBP fusion) | |||||||||
Components | Chimera of Maltose-binding periplasmic protein and Argonaute 2 | |||||||||
Keywords | GENE REGULATION / deviant OB fold / RNAi | |||||||||
Function / homology | Function and homology information detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) Drosophila melanogaster (fruit fly) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Song, J.J. / Liu, J. / Tolia, N.H. / Schneiderman, J. / Smith, S.K. / Martienssen, R.A. / Hannon, G.J. / Joshua-Tor, L. | |||||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2003 Title: The crystal structure of the Argonaute2 PAZ domain reveals an RNA binding motif in RNAi effector complexes. Authors: Song, J.J. / Liu, J. / Tolia, N.H. / Schneiderman, J. / Smith, S.K. / Martienssen, R.A. / Hannon, G.J. / Joshua-Tor, L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1r6z.cif.gz | 274.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r6z.ent.gz | 225.8 KB | Display | PDB format |
PDBx/mmJSON format | 1r6z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1r6z_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 1r6z_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 1r6z_validation.xml.gz | 57.7 KB | Display | |
Data in CIF | 1r6z_validation.cif.gz | 78.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r6/1r6z ftp://data.pdbj.org/pub/pdb/validation_reports/r6/1r6z | HTTPS FTP |
-Related structure data
Related structure data | 1anfS 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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-Components
#1: Protein | Mass: 56466.988 Da / Num. of mol.: 3 Fragment: MBP (residues 28-392) fused with Argonaute2 PAZ domain (residues 591-726) Source method: isolated from a genetically manipulated source Details: The construct is a fusion of E.coli MBP (residues 28-392) and D.melanogaster Argonaute2 PAZ domain (residues 591-726). Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Drosophila melanogaster (fruit fly) Genus: Escherichia, Drosophila / Species: , / Strain: , / Gene: MALE, Argonaute 2 CG7439-PB / Plasmid: modified pMAL_c2x / Production host: Escherichia coli (E. coli) / Strain (production host): BL21RIL References: UniProt: P02928, GenBank: 23093413, UniProt: P0AEX9*PLUS #2: Polysaccharide | #3: Chemical | ChemComp-NI / #4: 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: 2.61 Å3/Da / Density % sol: 52.92 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG2KMME, NiCl2, TrisHCl, NaF, meso-erythritol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 17 ℃ / pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 42457 / Num. obs: 41500 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 50.8 Å2 / Rsym value: 0.105 / Net I/σ(I): 12.74 |
Reflection shell | Resolution: 2.8→2.9 Å / Mean I/σ(I) obs: 1.756 / Num. unique all: 3383 / Rsym value: 0.548 / % possible all: 78.9 |
Reflection | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 50 Å / Num. measured all: 172206 / Rmerge(I) obs: 0.105 |
Reflection shell | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 2.9 Å / % possible obs: 78.9 % / Num. unique obs: 3383 / Rmerge(I) obs: 0.548 / Mean I/σ(I) obs: 1.76 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ANF(no sugar, no waters) Resolution: 2.8→44.91 Å / Isotropic thermal model: Isotropic / Cross valid method: Rfree / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 48.6 Å2 | ||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→44.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.024
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Software | *PLUS Name: CNS / Version: 1.1 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.801 Å / Lowest resolution: 50 Å / Num. reflection obs: 39394 / % reflection Rfree: 5 % / Rfactor Rfree: 0.2809 / Rfactor Rwork: 0.2268 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |