+Open data
-Basic information
Entry | Database: PDB / ID: 5k17 | ||||||
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Title | Crystal structure of CREN7-DSDNA (GTGATCGC) complex | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / PROTEIN-DNA COMPLEX / BETA-SHEET / DNA-BINDING / METHYLATION / DNA BINDING PROTEIN-DNA COMPLEX | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Sulfolobus solfataricus P2 (archaea) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Zhang, Z.F. / Gong, Y. | ||||||
Citation | Journal: PLoS ONE / Year: 2016 Title: Sequence-Dependent T:G Base Pair Opening in DNA Double Helix Bound by Cren7, a Chromatin Protein Conserved among Crenarchaea Authors: Tian, L. / Zhang, Z.F. / Wang, H. / Zhao, M. / Dong, Y. / Gong, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5k17.cif.gz | 58.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5k17.ent.gz | 38.4 KB | Display | PDB format |
PDBx/mmJSON format | 5k17.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k1/5k17 ftp://data.pdbj.org/pub/pdb/validation_reports/k1/5k17 | HTTPS FTP |
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-Related structure data
Related structure data | 5k07C 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: 6677.914 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus P2 (archaea) / Strain: P2 / Gene: creN7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q97ZE3 #2: DNA chain | Mass: 2442.616 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: 3.4 Å3/Da / Density % sol: 63.84 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion / Details: PEG1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97947 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 28, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97947 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 18763 / % possible obs: 99.9 % / Redundancy: 8.1 % / Net I/σ(I): 3.82 |
Reflection shell | Resolution: 2.1→2.18 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LWH Resolution: 2.1→38 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.959 / SU B: 4.132 / SU ML: 0.106 / Cross valid method: FREE R-VALUE / ESU R: 0.165 / ESU R Free: 0.139 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.666 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→38 Å
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Refine LS restraints |
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