[English] 日本語
Yorodumi- PDB-3ixh: X-ray crystal structure of the extended-spectrum AmpC Y221G mutan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ixh | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | X-ray crystal structure of the extended-spectrum AmpC Y221G mutant beta-lactamase in complex with cefotaxime at 2.3 Angstrom resolution | |||||||||
Components | Beta-lactamase | |||||||||
Keywords | HYDROLASE / serine hydrolase / beta-lactamase / cephalosporinase / extended-spectrum antibiotic resistance / Antibiotic resistance | |||||||||
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: 2.3 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3ixh.cif.gz | 151.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3ixh.ent.gz | 119.4 KB | Display | PDB format |
PDBx/mmJSON format | 3ixh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ixh_validation.pdf.gz | 813.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3ixh_full_validation.pdf.gz | 821.3 KB | Display | |
Data in XML | 3ixh_validation.xml.gz | 28.2 KB | Display | |
Data in CIF | 3ixh_validation.cif.gz | 39.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ix/3ixh ftp://data.pdbj.org/pub/pdb/validation_reports/ix/3ixh | HTTPS FTP |
-Related structure data
Related structure data | 3iwiC 3iwoC 3iwqC 3ixbC 3ixdC 3ixgC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-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: Chemical | ChemComp-CEF / | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.04 % |
---|---|
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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 26, 2009 / 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: 2.3→86.822 Å / Num. all: 33810 / Num. obs: 33712 / % possible obs: 96.9 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.106 / Rsym value: 0.106 / Net I/σ(I): 13.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR |
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.891 / WRfactor Rfree: 0.248 / WRfactor Rwork: 0.194 / Occupancy max: 1 / Occupancy min: 0.01 / FOM work R set: 0.833 / SU B: 6.829 / SU ML: 0.171 / SU R Cruickshank DPI: 0.372 / SU Rfree: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 0.372 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 max: 80.75 Å2 / Biso mean: 29.186 Å2 / Biso min: 7.69 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→30 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.359 Å / Total num. of bins used: 20
|