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Yorodumi- PDB-1d02: CRYSTAL STRUCTURE OF MUNI RESTRICTION ENDONUCLEASE IN COMPLEX WIT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d02 | ||||||
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Title | CRYSTAL STRUCTURE OF MUNI RESTRICTION ENDONUCLEASE IN COMPLEX WITH COGNATE DNA | ||||||
Components |
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Keywords | HYDROLASE/DNA / ALPHA/BETA PROTEIN / PROTEIN-DNA COMPLEX / DISTORTED DOUBLE HELIX / HYDROLASE-DNA COMPLEX | ||||||
Function / homology | Function and homology information type II site-specific deoxyribonuclease / type II site-specific deoxyribonuclease activity / DNA restriction-modification system / DNA binding Similarity search - Function | ||||||
Biological species | Mycoplasma (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å | ||||||
Authors | Deibert, M. / Grazulis, S. / Janulaitis, A. / Siksnys, V. / Huber, R. | ||||||
Citation | Journal: EMBO J. / Year: 1999 Title: Crystal structure of MunI restriction endonuclease in complex with cognate DNA at 1.7 A resolution. Authors: Deibert, M. / Grazulis, S. / Janulaitis, A. / Siksnys, V. / Huber, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d02.cif.gz | 116.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d02.ent.gz | 87.1 KB | Display | PDB format |
PDBx/mmJSON format | 1d02.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d0/1d02 ftp://data.pdbj.org/pub/pdb/validation_reports/d0/1d02 | 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: DNA chain | Mass: 3045.005 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: DECAMERIC OLIGONUCLEOTIDE 5'-DS(GPCPCPAPAPTPTPGPGPC) WAS SYNTHESIZED WITH STANDARD PROCEDURES #2: Protein | Mass: 23376.451 Da / Num. of mol.: 2 / Mutation: D83A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycoplasma (bacteria) / Genus: Mycoplasma / Production host: Escherichia coli (E. coli) / Strain (production host): ER2267 References: UniProt: P43642, type II site-specific deoxyribonuclease #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 | Density Matthews: 2.42 Å3/Da / Density % sol: 49.25 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: PEG 8000, CALCIUM CHLORIDE, SODIUM CHLORIDE, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K | ||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 54 % | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.006 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.006 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→8 Å / Num. all: 177834 / Num. obs: 56945 / % possible obs: 93.6 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Rmerge(I) obs: 0.052 |
Reflection | *PLUS Num. measured all: 177834 |
Reflection shell | *PLUS % possible obs: 84 % |
-Processing
Software |
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Refinement | Resolution: 1.7→8 Å / σ(F): 2 Stereochemistry target values: ENGH & HUBER (PROTEIN), PARKINSON (DNA)
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Refinement step | Cycle: LAST / Resolution: 1.7→8 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.18 / Rfactor Rwork: 0.18 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |