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- PDB-2z3h: Crystal structure of blasticidin S deaminase (BSD) complexed with... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2z3h | ||||||
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Title | Crystal structure of blasticidin S deaminase (BSD) complexed with deaminohydroxy blasticidin S | ||||||
![]() | Blasticidin-S deaminase | ||||||
![]() | HYDROLASE / CYTIDINE DEAMINASE FAMILY / ZINC / TETRAMER | ||||||
Function / homology | ![]() blasticidin-S deaminase / blasticidin-S deaminase activity / cytidine deaminase activity / response to antibiotic / zinc ion binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kumasaka, T. / Yamamoto, M. / Furuichi, M. / Nakasako, M. / Kimura, M. / Yamaguchi, I. / Ueki, T. | ||||||
![]() | ![]() Title: Crystal structures of blasticidin S deaminase (BSD): implications for dynamic properties of catalytic zinc Authors: Kumasaka, T. / Yamamoto, M. / Furuichi, M. / Nakasako, M. / Teh, A.H. / Kimura, M. / Yamaguchi, I. / Ueki, T. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Crystallization and Preliminary X-Ray Diffraction Studies of Blasticidin S Deaminase from Aspergillus Terreus Authors: Nakasako, M. / Kimura, M. / Yamaguchi, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 123.8 KB | Display | ![]() |
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PDB format | ![]() | 95.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 29.1 KB | Display | |
Data in CIF | ![]() | 42.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1wn5SC ![]() 1wn6C ![]() 2z3gC ![]() 2z3iC ![]() 2z3jC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 13478.245 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-BLO / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.85 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% PEG8000, 0.1M SODIUM CACODYLATE, 50MM MAGNESIUM CHLORIDE, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE |
Radiation | Monochromator: DIAMOND (400) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 89147 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.091 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1WN5 Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.957 / SU B: 0.985 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.065 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.88 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.54 Å / Total num. of bins used: 20
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