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Yorodumi- PDB-4x53: Structure of the class D Beta-Lactamase OXA-160 V130D in Acyl-Enz... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4x53 | |||||||||
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Title | Structure of the class D Beta-Lactamase OXA-160 V130D in Acyl-Enzyme Complex with Aztreonam | |||||||||
Components | Class D beta-lactamase OXA-160 | |||||||||
Keywords | HYDROLASE / Carbapenemase / Antibiotic | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Acinetobacter baumannii (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Clasman, J.R. / June, C.M. / Powers, R.A. / Leonard, D.A. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Biochemistry / Year: 2015 Title: Structural Basis of Activity against Aztreonam and Extended Spectrum Cephalosporins for Two Carbapenem-Hydrolyzing Class D beta-Lactamases from Acinetobacter baumannii. Authors: Mitchell, J.M. / Clasman, J.R. / June, C.M. / Kaitany, K.C. / LaFleur, J.R. / Taracila, M.A. / Klinger, N.V. / Bonomo, R.A. / Wymore, T. / Szarecka, A. / Powers, R.A. / Leonard, D.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4x53.cif.gz | 67.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4x53.ent.gz | 47.7 KB | Display | PDB format |
PDBx/mmJSON format | 4x53.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4x53_validation.pdf.gz | 783.2 KB | Display | wwPDB validaton report |
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Full document | 4x53_full_validation.pdf.gz | 786.6 KB | Display | |
Data in XML | 4x53_validation.xml.gz | 13 KB | Display | |
Data in CIF | 4x53_validation.cif.gz | 18.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x5/4x53 ftp://data.pdbj.org/pub/pdb/validation_reports/x5/4x53 | HTTPS FTP |
-Related structure data
Related structure data | 4x55C 4x56C 3paeS 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 27680.771 Da / Num. of mol.: 1 / Mutation: V130D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: blaOXA-160 / Plasmid: pET 24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: D2XKK9 |
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#2: Chemical | ChemComp-AZR / |
#3: Chemical | ChemComp-BCT / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.13 Å3/Da / Density % sol: 70.25 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M HEPES sodium, 2% v/v polyethylene glycol 400, 2.0 M ammonium sulfate, pH 7.5 PH range: 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0782 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 6, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0782 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→102.5 Å / Num. obs: 21201 / % possible obs: 100 % / Redundancy: 8 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 21 |
Reflection shell | Resolution: 2.302→2.309 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.614 / Mean I/σ(I) obs: 3.5 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3PAE Resolution: 2.3→72.44 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.414 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.172 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.751 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→72.44 Å
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Refine LS restraints |
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