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- PDB-1ewj: CRYSTAL STRUCTURE OF BLEOMYCIN-BINDING PROTEIN COMPLEXED WITH BLE... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ewj | ||||||
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Title | CRYSTAL STRUCTURE OF BLEOMYCIN-BINDING PROTEIN COMPLEXED WITH BLEOMYCIN | ||||||
![]() | BLEOMYCIN RESISTANCE DETERMINANT | ||||||
![]() | ANTIBIOTIC INHIBITOR / bleomycin-binding protein / bleomycin / antibiotics resistance / homodimer | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Maruyama, M. / Kumagai, T. / Matoba, Y. / Hata, Y. / Sugiyama, M. | ||||||
![]() | ![]() Title: Crystal structures of the transposon Tn5-carried bleomycin resistance determinant uncomplexed and complexed with bleomycin. Authors: Maruyama, M. / Kumagai, T. / Matoba, Y. / Hayashida, M. / Fujii, T. / Hata, Y. / Sugiyama, M. #1: ![]() Title: The 1.7 A Crystal structure of a bleomycin resistance protein encoded on the transposon Tn5 Authors: Maruyama, M. / Matoba, Y. / Kumagai, T. / Sugiyama, M. #2: ![]() Title: Crystallization and preliminary X-ray diffraction studies of bleomycin-binding protein encoded on the transposon Tn5 Authors: Kumagai, T. / Maruyama, M. / Matoba, Y. / Kawano, Y. / Sugiyama, M. #3: ![]() Title: The 1.5 A crystal structure of a bleomycin resistance determinant from bleomycin-producing Streptomyces verticillus Authors: Kawano, Y. / Kumagai, T. / Muta, K. / Matoba, Y. / Sugiyama, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 214.7 KB | Display | ![]() |
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PDB format | ![]() | 176.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 973.6 KB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 36.2 KB | Display | |
Data in CIF | ![]() | 42.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Details | The biological assembly is a homodimer |
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Components
#1: Protein | Mass: 14084.935 Da / Num. of mol.: 8 / Fragment: CORE DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Chemical | ChemComp-BLM / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.5 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: PEG 8000, ammonium sulfate, magnesium chloride, 2-(N-morpholino)-etanesulfonic acid, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Mar 20, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→100 Å / Num. all: 31016 / Num. obs: 27188 / % possible obs: 70 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.03 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.125 / Net I/σ(I): 4.06 |
Reflection shell | Resolution: 2.5→2.75 Å / Rmerge(I) obs: 0.372 / Num. unique all: 7014 / % possible all: 56.9 |
Reflection | *PLUS % possible obs: 70.1 % / Num. measured all: 62934 |
Reflection shell | *PLUS % possible obs: 56.9 % |
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Processing
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Refinement | Resolution: 2.5→30 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 29.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.221 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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