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- PDB-3ws1: N288Q-N321Q mutant BETA-LACTAMASE DERIVED FROM CHROMOHALOBACTER S... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ws1 | ||||||
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Title | N288Q-N321Q mutant BETA-LACTAMASE DERIVED FROM CHROMOHALOBACTER SP.560 (Condition-1B) | ||||||
![]() | Beta-lactamase | ||||||
![]() | HYDROLASE / CEPHALOSPORINASE | ||||||
Function / homology | ![]() antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Arai, S. / Yonezawa, Y. / Okazaki, N. / Matsumoto, F. / Shimizu, R. / Yamada, M. / Adachi, M. / Tamada, T. / Tokunaga, H. / Ishibashi, M. ...Arai, S. / Yonezawa, Y. / Okazaki, N. / Matsumoto, F. / Shimizu, R. / Yamada, M. / Adachi, M. / Tamada, T. / Tokunaga, H. / Ishibashi, M. / Tokunaga, M. / Kuroki, R. | ||||||
![]() | ![]() Title: Structure of a highly acidic beta-lactamase from the moderate halophile Chromohalobacter sp. 560 and the discovery of a Cs(+)-selective binding site Authors: Arai, S. / Yonezawa, Y. / Okazaki, N. / Matsumoto, F. / Shibazaki, C. / Shimizu, R. / Yamada, M. / Adachi, M. / Tamada, T. / Kawamoto, M. / Tokunaga, H. / Ishibashi, M. / Blaber, M. / Tokunaga, M. / Kuroki, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 428.8 KB | Display | ![]() |
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PDB format | ![]() | 353.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.6 KB | Display | ![]() |
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Full document | ![]() | 463.1 KB | Display | |
Data in XML | ![]() | 44.2 KB | Display | |
Data in CIF | ![]() | 64.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3wrtC ![]() 3wrzSC ![]() 3ws0C ![]() 3ws2C ![]() 3ws4C ![]() 3ws5C 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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2 | ![]()
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3 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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Components
#1: Protein | Mass: 39596.098 Da / Num. of mol.: 3 / Fragment: UNP residues 22-388 / Mutation: N288Q, N321Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Crystal was grown in a solution containing 100mM MES-NaOH buffer (pH 6.5), 200mM Ca acetate hydrate and 18% PEG8000. Obtained crystal was soaked into a solution containing 100mM MES NaOH ...Details: Crystal was grown in a solution containing 100mM MES-NaOH buffer (pH 6.5), 200mM Ca acetate hydrate and 18% PEG8000. Obtained crystal was soaked into a solution containing 100mM MES NaOH buffer (pH 6.5), 200mM Ca acetate hydrate, 75mM NaCl, 25mM CsCl and 18% PEG8000., VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: ![]() ![]() | |||||||||
Detector | Type: RIGAKU SATURN A200 / Detector: CCD / Date: Jul 25, 2013 | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.8→50 Å / Num. obs: 92243 / % possible obs: 99.2 % / Redundancy: 5.7 % / Biso Wilson estimate: 14.4 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 18.4 | |||||||||
Reflection shell | Resolution: 1.8→1.91 Å / Rmerge(I) obs: 0.308 / Mean I/σ(I) obs: 3.78 / % possible all: 98.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3WRZ Resolution: 1.8→37.68 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.356 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 31.404 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→37.68 Å
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Refine LS restraints |
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