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Yorodumi- PDB-5jgh: Crystal structure of the mitochondrial DNA packaging protein Abf2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jgh | ||||||
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Title | Crystal structure of the mitochondrial DNA packaging protein Abf2p in complex with DNA at 2.6 Angstrom resolution | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / DNA binding protein DNA packaging | ||||||
Function / homology | Function and homology information mitochondrial chromosome packaging / mitochondrial chromosome / mitochondrion inheritance / mitochondrial genome maintenance / DNA binding, bending / mitochondrial nucleoid / mitochondrion / DNA binding / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Chakraborty, A. / Lyonnais, S. / Sola, M. | ||||||
Funding support | Spain, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2017 Title: DNA structure directs positioning of the mitochondrial genome packaging protein Abf2p. Authors: Chakraborty, A. / Lyonnais, S. / Battistini, F. / Hospital, A. / Medici, G. / Prohens, R. / Orozco, M. / Vilardell, J. / Sola, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jgh.cif.gz | 225 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jgh.ent.gz | 181.4 KB | Display | PDB format |
PDBx/mmJSON format | 5jgh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jgh_validation.pdf.gz | 500.4 KB | Display | wwPDB validaton report |
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Full document | 5jgh_full_validation.pdf.gz | 520.2 KB | Display | |
Data in XML | 5jgh_validation.xml.gz | 30.7 KB | Display | |
Data in CIF | 5jgh_validation.cif.gz | 42.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jg/5jgh ftp://data.pdbj.org/pub/pdb/validation_reports/jg/5jgh | 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: 19486.270 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: ABF2, HIM1, YMR072W, YM9916.11 / Plasmid: pCri7a (pET-28a derivative) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLys / References: UniProt: Q02486 #2: DNA chain | Mass: 6719.397 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Oligos purchased from Biomers / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) #3: DNA chain | Mass: 6773.481 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Oligos purchased from Biomers / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) #4: Chemical | #5: 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: 2.52 Å3/Da / Density % sol: 51.27 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 20% PEG 4000, 0.2 M Ammonium Acetate, 0.1 M Tri-sodium Citrate pH 4.5 |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 30, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→48.05 Å / Num. obs: 38389 / % possible obs: 95 % / Redundancy: 2.3 % / CC1/2: 0.994 / Rmerge(I) obs: 0.112 / Net I/σ(I): 5.5 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 2.3 % / % possible all: 95.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PARTIAL MODEL FROM SAD PHASING Resolution: 2.6→48.048 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.35 / 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: 2.6→48.048 Å
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Refine LS restraints |
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LS refinement shell |
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