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Yorodumi- PDB-2wb0: 2.1 resolution structure of the C-terminal domain of the human ad... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wb0 | |||||||||
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Title | 2.1 resolution structure of the C-terminal domain of the human adenovirus 5 ssDNA binding protein | |||||||||
Components | E2A DNA-BINDING PROTEIN | |||||||||
Keywords | DNA BINDING PROTEIN / DNA-BINDING PROTEIN / SSDNA BINDING PROTEIN | |||||||||
Function / homology | Function and homology information viral DNA strand displacement replication / viral DNA genome replication / DNA duplex unwinding / DNA unwinding involved in DNA replication / positive regulation of DNA replication / viral capsid / single-stranded DNA binding / DNA-templated transcription / host cell nucleus / DNA binding ...viral DNA strand displacement replication / viral DNA genome replication / DNA duplex unwinding / DNA unwinding involved in DNA replication / positive regulation of DNA replication / viral capsid / single-stranded DNA binding / DNA-templated transcription / host cell nucleus / DNA binding / zinc ion binding / identical protein binding Similarity search - Function | |||||||||
Biological species | HUMAN ADENOVIRUS 5 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | |||||||||
Authors | Hendle, J. / Kanellopoulos, P.N. / Tucker, P.A. | |||||||||
Citation | Journal: To be Published Title: High Resolution Structures of the Adenovirus Single-Stranded DNA Binding Protein and the N512P Hinge-Region Mutant Authors: Hendle, J. / Kanellopoulos, P.N. / Tucker, P.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wb0.cif.gz | 86.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wb0.ent.gz | 63.6 KB | Display | PDB format |
PDBx/mmJSON format | 2wb0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wb0_validation.pdf.gz | 430.7 KB | Display | wwPDB validaton report |
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Full document | 2wb0_full_validation.pdf.gz | 440.7 KB | Display | |
Data in XML | 2wb0_validation.xml.gz | 18.9 KB | Display | |
Data in CIF | 2wb0_validation.cif.gz | 28.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wb/2wb0 ftp://data.pdbj.org/pub/pdb/validation_reports/wb/2wb0 | HTTPS FTP |
-Related structure data
Related structure data | 2wazC 1adt C: citing same article (ref.) 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: Protein | Mass: 39899.746 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DNA BINDING DOMAIN, RESIDUES 174-529 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HUMAN ADENOVIRUS 5 / Plasmid: PETM11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q2KS06, UniProt: P03265*PLUS | ||
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#2: Chemical | #3: 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: 2.42 Å3/Da / Density % sol: 48.83 % / Description: NONE |
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Crystal grow | pH: 5.8 / Details: pH 5.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.928 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRRORS |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.928 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→15 Å / Num. obs: 29937 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 21.3 |
Reflection shell | Resolution: 1.95→2.05 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 4.5 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ADT 1adt Resolution: 1.95→14.95 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.915 / SU B: 3.258 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. RESIDUES 299 TO 327 AND 456 TO 463 COULD NOT BE MODELLED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.45 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→14.95 Å
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Refine LS restraints |
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