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Yorodumi- PDB-4cj9: BurrH DNA-binding protein from Burkholderia rhizoxinica in its ap... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cj9 | ||||||
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Title | BurrH DNA-binding protein from Burkholderia rhizoxinica in its apo form | ||||||
Components | BURRH | ||||||
Keywords | TRANSCRIPTION / GENE TARGETING / PROTEIN-DNA INTERACTION | ||||||
Function / homology | TAL effector repeat / TAL effector repeat / Domain of unknown function DUF3447 / Ankyrin repeat region circular profile. / Ankyrin repeat-containing domain superfamily / double-stranded DNA binding / SELENIUM ATOM / Burkholderia TALE-like protein 1 Function and homology information | ||||||
Biological species | BURKHOLDERIA RHIZOXINICA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.214 Å | ||||||
Authors | Stella, S. / Molina, R. / Lopez-Mendez, B. / Campos-Olivas, R. / Duchateau, P. / Montoya, G. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Bud, a Helix-Loop-Helix DNA-Binding Domain for Genome Modification Authors: Stella, S. / Molina, R. / Lopez-Mendez, B. / Juillerat, A. / Bertonati, C. / Daboussi, F. / Campos-Olivas, R. / Duchateau, P. / Montoya, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cj9.cif.gz | 573.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cj9.ent.gz | 493.2 KB | Display | PDB format |
PDBx/mmJSON format | 4cj9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cj9_validation.pdf.gz | 436.7 KB | Display | wwPDB validaton report |
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Full document | 4cj9_full_validation.pdf.gz | 446.4 KB | Display | |
Data in XML | 4cj9_validation.xml.gz | 57.3 KB | Display | |
Data in CIF | 4cj9_validation.cif.gz | 84.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cj/4cj9 ftp://data.pdbj.org/pub/pdb/validation_reports/cj/4cj9 | HTTPS FTP |
-Related 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: 83517.117 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BURKHOLDERIA RHIZOXINICA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: E5AV36*PLUS #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 41 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97974 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97974 Å / Relative weight: 1 |
Reflection | Resolution: 2.21→46.08 Å / Num. obs: 79217 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 39.02 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.21→2.33 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.4 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2.214→63.492 Å / SU ML: 0.25 / σ(F): 0.27 / Phase error: 23.75 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.214→63.492 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -1.7557 Å / Origin y: 36.4997 Å / Origin z: 132.5729 Å
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Refinement TLS group | Selection details: ALL |