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Yorodumi- PDB-7c0j: Crystal structure of chimeric mutant of GH5 in complex with Z-DNA -
+Open data
-Basic information
Entry | Database: PDB / ID: 7c0j | ||||||
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Title | Crystal structure of chimeric mutant of GH5 in complex with Z-DNA | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / GH5 / Protein-DNA complex / protein engineering / Z-DNA binding protein / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information somatic diversification of immune receptors via somatic mutation / negative regulation of post-transcriptional gene silencing by regulatory ncRNA / C6 deamination of adenosine / Formation of editosomes by ADAR proteins / double-stranded RNA adenine deaminase / tRNA-specific adenosine deaminase activity / supraspliceosomal complex / double-stranded RNA adenosine deaminase activity / negative regulation of protein kinase activity by regulation of protein phosphorylation / base conversion or substitution editing ...somatic diversification of immune receptors via somatic mutation / negative regulation of post-transcriptional gene silencing by regulatory ncRNA / C6 deamination of adenosine / Formation of editosomes by ADAR proteins / double-stranded RNA adenine deaminase / tRNA-specific adenosine deaminase activity / supraspliceosomal complex / double-stranded RNA adenosine deaminase activity / negative regulation of protein kinase activity by regulation of protein phosphorylation / base conversion or substitution editing / hematopoietic stem cell homeostasis / response to interferon-alpha / adenosine to inosine editing / negative regulation of DNA recombination / RISC complex assembly / negative regulation of hepatocyte apoptotic process / pre-miRNA processing / definitive hemopoiesis / chromosome condensation / negative regulation of type I interferon-mediated signaling pathway / hepatocyte apoptotic process / positive regulation of viral genome replication / RNA processing / hematopoietic progenitor cell differentiation / nucleosomal DNA binding / protein export from nucleus / erythrocyte differentiation / response to virus / PKR-mediated signaling / mRNA processing / cellular response to virus / osteoblast differentiation / structural constituent of chromatin / protein import into nucleus / nucleosome / Interferon alpha/beta signaling / double-stranded RNA binding / nucleosome assembly / chromatin organization / double-stranded DNA binding / defense response to virus / innate immune response / nucleolus / DNA binding / RNA binding / nucleoplasm / membrane / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.75 Å | ||||||
Authors | Choi, H.J. / Park, C.H. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2020 Title: Dual conformational recognition by Z-DNA binding protein is important for the B-Z transition process. Authors: Park, C. / Zheng, X. / Park, C.Y. / Kim, J. / Lee, S.K. / Won, H. / Choi, J. / Kim, Y.G. / Choi, H.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7c0j.cif.gz | 78.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7c0j.ent.gz | 54.1 KB | Display | PDB format |
PDBx/mmJSON format | 7c0j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7c0j_validation.pdf.gz | 442.4 KB | Display | wwPDB validaton report |
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Full document | 7c0j_full_validation.pdf.gz | 442.5 KB | Display | |
Data in XML | 7c0j_validation.xml.gz | 6.7 KB | Display | |
Data in CIF | 7c0j_validation.cif.gz | 8.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c0/7c0j ftp://data.pdbj.org/pub/pdb/validation_reports/c0/7c0j | HTTPS FTP |
-Related structure data
Related structure data | 7c0iC 1hstS 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: 8109.267 Da / Num. of mol.: 2 / Mutation: K41G,S42E,R43G,K53A,R95A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken), (gene. exp.) Homo sapiens (human) Gene: ADAR1 / Production host: Escherichia coli (E. coli) / References: UniProt: P02259, UniProt: P55265 #2: DNA chain | Mass: 2114.398 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: 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: 2.04 Å3/Da / Density % sol: 39.56 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: MES pH 6.0, PEG 4000, ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 29, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.7→50 Å / Num. obs: 4625 / % possible obs: 99.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.054 / Rrim(I) all: 0.104 / Χ2: 0.993 / Net I/σ(I): 7.4 / Num. measured all: 16934 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HST Resolution: 2.75→28.876 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 21.33 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 115.32 Å2 / Biso mean: 42.9232 Å2 / Biso min: 15.44 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.75→28.876 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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