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Yorodumi- PDB-1yf2: Three-dimensional structure of DNA sequence specificity (S) subun... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yf2 | ||||||
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Title | Three-dimensional structure of DNA sequence specificity (S) subunit of a type I restriction-modification enzyme and its functional implications | ||||||
Components | Type I restriction-modification enzyme, S subunit | ||||||
Keywords | HYDROLASE REGULATOR / Type I restriction modification enzyme / S-subunit / Structural genomics / PSI / Protein Structure Initiative / Berkeley Structural Genomics Center / BSGC | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å | ||||||
Authors | Kim, J.S. / Degiovanni, A. / Jancarik, J. / Adams, P.D. / Yokota, H.A. / Kim, R. / Kim, S.H. / Berkeley Structural Genomics Center (BSGC) | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2005 Title: Crystal structure of DNA sequence specificity subunit of a type I restriction-modification enzyme and its functional implications. Authors: Kim, J.S. / Degiovanni, A. / Jancarik, J. / Adams, P.D. / Yokota, H. / Kim, R. / Kim, S.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yf2.cif.gz | 184.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yf2.ent.gz | 147.9 KB | Display | PDB format |
PDBx/mmJSON format | 1yf2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yf2_validation.pdf.gz | 424.3 KB | Display | wwPDB validaton report |
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Full document | 1yf2_full_validation.pdf.gz | 452.9 KB | Display | |
Data in XML | 1yf2_validation.xml.gz | 37.1 KB | Display | |
Data in CIF | 1yf2_validation.cif.gz | 52.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yf/1yf2 ftp://data.pdbj.org/pub/pdb/validation_reports/yf/1yf2 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | The biological assembly is a monomer |
-Components
#1: Protein | Mass: 48639.555 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Strain: DSM 2661 / Plasmid details: pET23a derivatized expression vector / Plasmid: pB3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q57594 #2: 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: 3.74 Å3/Da / Density % sol: 66.5 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: PEG 3000, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 12, 2004 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.21→50 Å / Num. all: 69051 / Num. obs: 59867 / Observed criterion σ(F): 1.2 / Observed criterion σ(I): 1.2 / Biso Wilson estimate: 49.2 Å2 |
Reflection shell | Resolution: 2.21→2.29 Å / % possible all: 26.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.4→48.52 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 361731.16 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 60.6471 Å2 / ksol: 0.311875 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 74.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→48.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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