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Yorodumi- PDB-3iwi: X-ray crystal structure of the extended-spectrum AmpC omega loop ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3iwi | ||||||
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Title | X-ray crystal structure of the extended-spectrum AmpC omega loop insertion (H210AAA) mutant beta-lactamase at 1.64 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.64 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 | 3iwi.cif.gz | 170.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3iwi.ent.gz | 133.7 KB | Display | PDB format |
PDBx/mmJSON format | 3iwi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iw/3iwi ftp://data.pdbj.org/pub/pdb/validation_reports/iw/3iwi | HTTPS FTP |
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-Related structure data
Related structure data | 3iwoC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 39801.156 Da / Num. of mol.: 2 / Mutation: H210AAA insertion 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: Chemical | ChemComp-PO4 / | #3: 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: 2.54 Å3/Da / Density % sol: 51.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1.7M KPi, pH 8.0, 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: Oct 11, 2005 / 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: 1.64→88.161 Å / Num. all: 97371 / Num. obs: 97338 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 1.64→1.73 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.325 / % possible all: 99.9 |
-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1KE4 Resolution: 1.64→30 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / Occupancy max: 1 / Occupancy min: 0 / SU B: 1.522 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.087 / 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: 17.393 Å2
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Refinement step | Cycle: LAST / Resolution: 1.64→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.64→1.682 Å / Total num. of bins used: 20
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