+Open data
-Basic information
Entry | Database: PDB / ID: 5wvy | ||||||
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Title | The crystal structure of Cren7 mutant L28V in complex with dsDNA | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / BETA-SHEET / DNA BINDING / DNA BINDING PROTEIN-DNA COMPLEX / Crenarchaeal chromatin protein | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Sulfolobus solfataricus (archaea) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Zhang, Z.F. / Zhao, M.H. / Wang, L. / Chen, Y.Y. / Dong, Y.H. / Gong, Y. / Huang, L. | ||||||
Citation | Journal: Biochem. J. / Year: 2017 Title: Roles of Leu28 side chain intercalation in the interaction between Cren7 and DNA Authors: Zhang, Z. / Zhao, M. / Wang, L. / Chen, Y. / Dong, Y. / Gong, Y. / Huang, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wvy.cif.gz | 60.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wvy.ent.gz | 40.3 KB | Display | PDB format |
PDBx/mmJSON format | 5wvy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5wvy_validation.pdf.gz | 438.8 KB | Display | wwPDB validaton report |
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Full document | 5wvy_full_validation.pdf.gz | 438.7 KB | Display | |
Data in XML | 5wvy_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | 5wvy_validation.cif.gz | 14.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wv/5wvy ftp://data.pdbj.org/pub/pdb/validation_reports/wv/5wvy | HTTPS FTP |
-Related structure data
Related structure data | 5wvwC 5wvzC 5wwcC 3lwhS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 6663.887 Da / Num. of mol.: 2 / Mutation: L28V 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: creN7, SSO6901 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA 2 (DE3) / References: UniProt: Q97ZE3 #2: DNA chain | Mass: 2426.617 Da / Num. of mol.: 4 / 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: 3.52 Å3/Da / Density % sol: 65.04 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.1M Sodium acetate pH4.6, 40% PEG200 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 11, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 22094 / % possible obs: 99.3 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 37.3 |
Reflection shell | Resolution: 2→2.03 Å / Rmerge(I) obs: 0.543 / Mean I/σ(I) obs: 2 / % possible all: 91 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LWH Resolution: 2→50 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / Phase error: 27.59
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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LS refinement shell |
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