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Yorodumi- PDB-3ws5: N288Q-N321Q mutant BETA-LACTAMASE DERIVED FROM CHROMOHALOBACTER S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ws5 | ||||||
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Title | N288Q-N321Q mutant BETA-LACTAMASE DERIVED FROM CHROMOHALOBACTER SP.560 (Condition-2B) | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / CEPHALOSPORINASE | ||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic / metal ion binding Similarity search - Function | ||||||
Biological species | Chromohalobacter sp. 560 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | 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. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ws5.cif.gz | 410.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ws5.ent.gz | 338.1 KB | Display | PDB format |
PDBx/mmJSON format | 3ws5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ws/3ws5 ftp://data.pdbj.org/pub/pdb/validation_reports/ws/3ws5 | HTTPS FTP |
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-Related structure data
Related structure data | 3wrtC 3wrzSC 3ws0C 3ws1C 3ws2C 3ws4C C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / Refine code: 0
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.) Chromohalobacter sp. 560 (bacteria) / Gene: bla / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): E. COLI BL21 STAR (DE3) / References: UniProt: Q76LX5, beta-lactamase #2: Chemical | ChemComp-SR / | #3: Chemical | #4: Chemical | ChemComp-CA / | #5: 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: 2.13 Å3/Da / Density % sol: 42.14 % |
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Crystal grow | Temperature: 293 K / pH: 7 Details: Crystal was grown in a solution containing 100mM MES-NaOH buffer (pH 6.5), 200mM Ca acetate hydrate and 18% PEG 8000. Obtained crystal w as soaked into a solution containing 100 mM MES-NaOH ...Details: Crystal was grown in a solution containing 100mM MES-NaOH buffer (pH 6.5), 200mM Ca acetate hydrate and 18% PEG 8000. Obtained crystal w as soaked into a solution containing 100 mM MES-NaOH buffer (pH 6.5), 100mM Ca acetate, 100mM Sr acetate and 18% PEG8000., VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1.000, 0.769 | |||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 21, 2013 | |||||||||
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.8→50 Å / Num. obs: 22606 / % possible obs: 90.6 % / Redundancy: 2.9 % / Biso Wilson estimate: 31.5 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 19.5 | |||||||||
Reflection shell | Resolution: 2.8→2.85 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 7.96 / % possible all: 92.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WRZ Resolution: 2.8→29.59 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.908 / SU B: 19.862 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R Free: 0.076 / 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: 44.034 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→29.59 Å
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Refine LS restraints |
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