+Open data
-Basic information
Entry | Database: PDB / ID: 8jvq | ||||||||||||
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Title | Crystal structure of the dimeric RIFT fold protein Ph1_DG | ||||||||||||
Components | Ph1_DG | ||||||||||||
Keywords | DNA BINDING PROTEIN / RIFT barrel | ||||||||||||
Function / homology | CITRIC ACID Function and homology information | ||||||||||||
Biological species | synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.401 Å | ||||||||||||
Authors | Yagi, S. / Tagami, S. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: To Be Published Title: Missing-link fold reveals the evolutionary pathway between RNA polymerase and ribosomal proteins Authors: Yagi, S. / Tagami, S. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8jvq.cif.gz | 30.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jvq.ent.gz | 19.5 KB | Display | PDB format |
PDBx/mmJSON format | 8jvq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8jvq_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8jvq_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8jvq_validation.xml.gz | 5 KB | Display | |
Data in CIF | 8jvq_validation.cif.gz | 6.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jv/8jvq ftp://data.pdbj.org/pub/pdb/validation_reports/jv/8jvq | HTTPS FTP |
-Related structure data
Related structure data | 8jvnC 8jvoC 8jvpC 8jvrC 8jvsC 8jvtC 8jvuC 8jvvC 8jvwC 8jvxC 8jvyC 8jvzC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein/peptide | Mass: 4681.695 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria) |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-CIT / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 3200mM Ammonium sulfate, 100mM Citric acid/Sodium hydroxide pH5.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Apr 22, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. obs: 14659 / % possible obs: 99.2 % / Redundancy: 11.1 % / CC1/2: 1 / Net I/σ(I): 12.45 |
Reflection shell | Resolution: 1.4→1.5 Å / Num. unique obs: 2362 / CC1/2: 0.99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.401→26.518 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.13 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.401→26.518 Å
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Refine LS restraints |
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LS refinement shell |
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