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Yorodumi- PDB-1kcf: Crystal Structure of the Yeast Mitochondrial Holliday Junction Re... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kcf | ||||||
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Title | Crystal Structure of the Yeast Mitochondrial Holliday Junction Resolvase, Ydc2 | ||||||
Components | HYPOTHETICAL 30.2 KD PROTEIN C25G10.02 IN CHROMOSOME I | ||||||
Keywords | HYDROLASE / beta-alpha-beta motif / RuvC resolvase family | ||||||
Function / homology | Function and homology information mitochondrial chromosome / crossover junction endodeoxyribonuclease / crossed form four-way junction DNA binding / flap-structured DNA binding / crossover junction DNA endonuclease activity / Y-form DNA binding / mitochondrial DNA metabolic process / mitochondrial genome maintenance / four-way junction DNA binding / DNA endonuclease activity ...mitochondrial chromosome / crossover junction endodeoxyribonuclease / crossed form four-way junction DNA binding / flap-structured DNA binding / crossover junction DNA endonuclease activity / Y-form DNA binding / mitochondrial DNA metabolic process / mitochondrial genome maintenance / four-way junction DNA binding / DNA endonuclease activity / mitochondrion / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Single Wavelength Anomalous Dispersion / Resolution: 2.3 Å | ||||||
Authors | Ceschini, S. / Keeley, A. / McAlister, M.S.B. / Oram, M. / Phelan, J. / Pearl, L.H. / Tsaneva, I.R. / Barrett, T.E. | ||||||
Citation | Journal: EMBO J. / Year: 2001 Title: Crystal structure of the fission yeast mitochondrial Holliday junction resolvase Ydc2. Authors: Ceschini, S. / Keeley, A. / McAlister, M.S. / Oram, M. / Phelan, J. / Pearl, L.H. / Tsaneva, I.R. / Barrett, T.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kcf.cif.gz | 109.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kcf.ent.gz | 85 KB | Display | PDB format |
PDBx/mmJSON format | 1kcf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kc/1kcf ftp://data.pdbj.org/pub/pdb/validation_reports/kc/1kcf | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 30247.793 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Gene: SPAC25G10.02 / Plasmid: pET21a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 References: UniProt: Q10423, Hydrolases; Acting on ester bonds #2: Chemical | #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 |
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Crystal grow |
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Crystal grow | *PLUS Method: batch method | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 31, 2001 / Details: Mirrors |
Radiation | Monochromator: Sagitally focused Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→29.34 Å / Num. all: 35212 / Num. obs: 31239 / % possible obs: 91.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 43.4 Å2 / Rmerge(I) obs: 0.04 / Rsym value: 0.034 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 3.6 / Num. unique all: 4787 / Rsym value: 0.17 / % possible all: 90.5 |
Reflection | *PLUS Redundancy: 3.4 % / Rmerge(I) obs: 0.034 |
Reflection shell | *PLUS Rmerge(I) obs: 0.219 |
-Processing
Software |
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Refinement | Method to determine structure: Single Wavelength Anomalous Dispersion Resolution: 2.3→29.34 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1517194.37 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Used bulk solvent correction, simulated annealing, energy minimization, overall and indvidual B-factor refinement. A maximum likelihood refinent target was also used.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 69.7635 Å2 / ksol: 0.366887 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→29.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.238 / Rfactor Rfree: 0.27 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 55.7 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.302 / % reflection Rfree: 4.9 % / Rfactor Rwork: 0.268 |