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Yorodumi- PDB-4r55: The crystal structure of a Cren7 mutant protein GR and dsDNA complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 4r55 | ||||||
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Title | The crystal structure of a Cren7 mutant protein GR and dsDNA complex | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / BETA-SHEET / DNA BINDING / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Sulfolobus solfataricus P2 (archaea) synthetic (others) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Zhang, Z.F. / Gong, Y. / Chen, Y.Y. / Li, H.B. / Huang, L. | ||||||
Citation | Journal: Extremophiles / Year: 2015 Title: Insights into the interaction between Cren7 and DNA: the role of loop beta 3-beta 4 Authors: Zhang, Z.F. / Gong, Y. / Chen, Y.Y. / Li, H.B. / Huang, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4r55.cif.gz | 34.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4r55.ent.gz | 20.8 KB | Display | PDB format |
PDBx/mmJSON format | 4r55.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4r55_validation.pdf.gz | 405.9 KB | Display | wwPDB validaton report |
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Full document | 4r55_full_validation.pdf.gz | 405.9 KB | Display | |
Data in XML | 4r55_validation.xml.gz | 5.5 KB | Display | |
Data in CIF | 4r55_validation.cif.gz | 7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r5/4r55 ftp://data.pdbj.org/pub/pdb/validation_reports/r5/4r55 | HTTPS FTP |
-Related structure data
Related structure data | 4r56C 3lwhS 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: 6194.311 Da / Num. of mol.: 1 / Mutation: DELETION Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus P2 (archaea) / Gene: creN7, SSO6901 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) plysS / References: UniProt: Q97ZE3 | ||
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#2: DNA chain | Mass: 2426.617 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic (others) #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: 2.18 Å3/Da / Density % sol: 43.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2M NH4Ac, 0.01M MgAc2, 0.05M sodium cacodylate trihydrate, 30% PEG 8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 17, 2013 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 9449 / Num. obs: 9402 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.7 % / Biso Wilson estimate: 12.9 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 40.6 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.084 / Mean I/σ(I) obs: 25.3 / Num. unique all: 918 / % possible all: 99 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LWH Resolution: 1.8→17 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.893 / SU B: 2.857 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.152 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.603 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→17 Å
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Refine LS restraints |
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