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Yorodumi- PDB-6iqc: Wild-type Programmed Cell Death 5 protein from Sulfolobus solfataricus -
+Open data
-Basic information
Entry | Database: PDB / ID: 6iqc | ||||||
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Title | Wild-type Programmed Cell Death 5 protein from Sulfolobus solfataricus | ||||||
Components | DNA-binding protein SSO0352 | ||||||
Keywords | DNA BINDING PROTEIN / Sulfolobus | ||||||
Function / homology | DNA-binding protein, archaeal / PDCD5-like / PDCD5-like superfamily / Double-stranded DNA-binding domain / DNA binding / cytosol / DNA-binding protein SSO0352 Function and homology information | ||||||
Biological species | Sulfolobus solfataricus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å | ||||||
Authors | Chen, C.Y. / Lin, K.F. / Hsu, C.Y. / Tsai, M.J. | ||||||
Funding support | Taiwan, 1items
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Citation | Journal: Acta Crystallogr F Struct Biol Commun / Year: 2019 Title: Crystal structure of the programmed cell death 5 protein from Sulfolobus solfataricus. Authors: Lin, K.F. / Hsu, J.Y. / Hsieh, D.L. / Tsai, M.J. / Yeh, C.H. / Chen, C.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6iqc.cif.gz | 38.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6iqc.ent.gz | 24.6 KB | Display | PDB format |
PDBx/mmJSON format | 6iqc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6iqc_validation.pdf.gz | 749.3 KB | Display | wwPDB validaton report |
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Full document | 6iqc_full_validation.pdf.gz | 750.6 KB | Display | |
Data in XML | 6iqc_validation.xml.gz | 7.8 KB | Display | |
Data in CIF | 6iqc_validation.cif.gz | 10.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iq/6iqc ftp://data.pdbj.org/pub/pdb/validation_reports/iq/6iqc | HTTPS FTP |
-Related structure data
Related structure data | 6iqoSC 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14078.048 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea) Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: SSO0352 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: Q980F8 |
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#2: Chemical | ChemComp-PG4 / |
#3: Chemical | ChemComp-NA / |
#4: 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: 1.76 Å3/Da / Density % sol: 30.2 % |
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Crystal grow | Temperature: 293 K / Method: liquid diffusion / pH: 6.9 / Details: 20% PEG 3350, 0.2M KSCN |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Mar 17, 2018 |
Radiation | Monochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→23.48 Å / Num. obs: 15594 / % possible obs: 98.1 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.015 / Net I/σ(I): 48.25 |
Reflection shell | Resolution: 1.5→1.55 Å / Rmerge(I) obs: 0.563 / Num. unique obs: 1552 / CC1/2: 0.891 / Rpim(I) all: 0.316 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6IQO Resolution: 1.49→23.48 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.921 / SU B: 2.227 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.12 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.423 Å2
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Refinement step | Cycle: 1 / Resolution: 1.49→23.48 Å
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Refine LS restraints |
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