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Yorodumi- PDB-5t7x: Crystal structure of HHV-4 EBNA1 DNA binding domain (patient-deri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5t7x | ||||||
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Title | Crystal structure of HHV-4 EBNA1 DNA binding domain (patient-derived, nasopharyngeal carcinoma) bound to DNA | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / Dimer / DNA / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information viral latency / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / regulation of DNA replication / endonuclease activity / DNA-binding transcription factor activity / host cell nucleus / positive regulation of DNA-templated transcription / DNA binding / identical protein binding Similarity search - Function | ||||||
Biological species | Human herpesvirus 4 (Epstein-Barr virus) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Malecka, K.A. / Messick, T.E. / Lieberman, P.M. | ||||||
Citation | Journal: Oncotarget / Year: 2017 Title: Carcinoma-risk variant of EBNA1 deregulates Epstein-Barr Virus episomal latency. Authors: Dheekollu, J. / Malecka, K. / Wiedmer, A. / Delecluse, H.J. / Chiang, A.K. / Altieri, D.C. / Messick, T.E. / Lieberman, P.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5t7x.cif.gz | 93.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5t7x.ent.gz | 66 KB | Display | PDB format |
PDBx/mmJSON format | 5t7x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t7/5t7x ftp://data.pdbj.org/pub/pdb/validation_reports/t7/5t7x | HTTPS FTP |
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-Related structure data
Related structure data | 1b3tS 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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Unit cell |
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-Components
#1: DNA chain | Mass: 5476.554 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Human herpesvirus 4 (strain B95-8) (Epstein-Barr virus (strain B95-8)) | ||
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#2: DNA chain | Mass: 5556.603 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Human herpesvirus 4 (strain B95-8) (Epstein-Barr virus (strain B95-8)) | ||
#3: Protein | Mass: 16332.018 Da / Num. of mol.: 2 / Fragment: UNP residues 459-507 Source method: isolated from a genetically manipulated source Details: patient-derived, nasopharyngeal carcinoma Source: (gene. exp.) Human herpesvirus 4 (strain B95-8) (Epstein-Barr virus (strain B95-8)) Strain: GD1 / Gene: EBNA1, BKRF1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3KSS4 #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: 2.51 Å3/Da / Density % sol: 50.96 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.2 M ammonium acetate, 0.15 M magnesium acetate tetrahydrate, 0.05 M Hepes, pH 7.0, 5% PEG 4000 Temp details: room temperature |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Aug 27, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. obs: 19350 / % possible obs: 98.7 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.198 / Net I/σ(I): 21.9 |
Reflection shell | Redundancy: 7.2 % / Rmerge(I) obs: 0.879 / Mean I/σ(I) obs: 7.4 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1B3T Resolution: 2.35→23.373 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.79
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→23.373 Å
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Refine LS restraints |
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LS refinement shell |
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