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Yorodumi- PDB-3iwo: X-ray crystal structure of the extended-spectrum AmpC Y221G mutan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3iwo | |||||||||
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Title | X-ray crystal structure of the extended-spectrum AmpC Y221G mutant beta-lactamase at 1.90 Angstrom resolution | |||||||||
Components | Beta-lactamase | |||||||||
Keywords | HYDROLASE / serine hydrolase / beta-lactamase / cephalosporinase / extended-spectrum antibiotic resistance / Antibiotic resistance / Periplasm | |||||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Rigid body refinement from wild-type structure / Resolution: 1.9 Å | |||||||||
Authors | Shoichet, B.K. / Thomas, V.L. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Structural bases for stability-function tradeoffs in antibiotic resistance. Authors: Thomas, V.L. / McReynolds, A.C. / Shoichet, B.K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3iwo.cif.gz | 165.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3iwo.ent.gz | 129 KB | Display | PDB format |
PDBx/mmJSON format | 3iwo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3iwo_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 3iwo_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 3iwo_validation.xml.gz | 33.2 KB | Display | |
Data in CIF | 3iwo_validation.cif.gz | 50.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iw/3iwo ftp://data.pdbj.org/pub/pdb/validation_reports/iw/3iwo | HTTPS FTP |
-Related structure data
Related structure data | 3iwiC 3iwqC 3ixbC 3ixdC 3ixgC 3ixhC 1ke4S 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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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 39481.801 Da / Num. of mol.: 2 / Mutation: Y221G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ampA, ampC, b4150, JW4111 / Plasmid: pOGO295 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00811, beta-lactamase #2: Polysaccharide | #3: Chemical | ChemComp-PO4 / | #4: 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: 2.53 Å3/Da / Density % sol: 51.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.7 Details: 1.7M KPi, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 31, 2008 / Details: mirrors |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11587 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→88.388 Å / Num. obs: 61926 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.277 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.277 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: Rigid body refinement from wild-type structure Starting model: PDB entry 1KE4 Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.938 / Occupancy max: 1 / Occupancy min: 0.01 / SU B: 2.543 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.124 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.663 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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