[English] 日本語
Yorodumi- PDB-1ecs: THE 1.7 A CRYSTAL STRUCTURE OF A BLEOMYCIN RESISTANCE DETERMINANT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ecs | ||||||
---|---|---|---|---|---|---|---|
Title | THE 1.7 A CRYSTAL STRUCTURE OF A BLEOMYCIN RESISTANCE DETERMINANT ENCODED ON THE TRANSPOSON TN5 | ||||||
Components | BLEOMYCIN RESISTANCE PROTEIN | ||||||
Keywords | ANTIBIOTIC INHIBITOR / ARM-EXCHANGE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Maruyama, M. / Matoba, Y. / Kumagai, T. / Sugiyama, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 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: Journal: FEBS Lett. / Year: 1999 Title: Characterizaton of the bleomycin resistance determinant encoded on the transposon Tn5 Authors: Kumagai, T. / Nakano, T. / Maruyama, M. / Mochizuki, H. / Sugiyama, M. #2: Journal: Acta Crystallogr.,Sect.D / Year: 1999 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. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1ecs.cif.gz | 63.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1ecs.ent.gz | 45.8 KB | Display | PDB format |
PDBx/mmJSON format | 1ecs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ecs_validation.pdf.gz | 381.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1ecs_full_validation.pdf.gz | 385.8 KB | Display | |
Data in XML | 1ecs_validation.xml.gz | 7 KB | Display | |
Data in CIF | 1ecs_validation.cif.gz | 10.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ec/1ecs ftp://data.pdbj.org/pub/pdb/validation_reports/ec/1ecs | HTTPS FTP |
-Related structure data
Related structure data | 1ewjC 1qtoS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 14012.873 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: TRANSPOSON TN5 / Plasmid: PKKTRP / Production host: Escherichia coli (E. coli) / References: UniProt: P13081 #2: Chemical | ChemComp-CA / | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
---|
-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.2 % | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 6000, calcium acetate, sodium cacodylate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||
Crystal | *PLUS Density % sol: 49 % | ||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 298 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 |
Detector | Type: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Feb 20, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→58.77 Å / Num. obs: 28095 / % possible obs: 92.4 % / Observed criterion σ(I): 1 / Redundancy: 10.5 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 1.7→1.77 Å / Redundancy: 3.46 % / Rmerge(I) obs: 0.253 / % possible all: 78.1 |
Reflection | *PLUS Num. measured all: 295760 |
Reflection shell | *PLUS % possible obs: 78.1 % |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: DIMERIC BLMA (1QTO) Resolution: 1.7→5 Å / Num. parameters: 8115 / Num. restraintsaints: 7896 / Stereochemistry target values: ENGH AND HUBER
| |||||||||||||||||||||||||||||||||
Refine analyze | Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2028.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→5 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||
Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.192 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|