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Yorodumi- PDB-4olg: Crystal structure of AmpC beta-lactamase in complex with covalent... -
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-Basic information
Entry | Database: PDB / ID: 4olg | ||||||
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Title | Crystal structure of AmpC beta-lactamase in complex with covalently bound N-formyl 7-aminocephalosporanic acid | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / AMPC BETA-LACTAMASE / CLASS / CEPHALOSPORINASE | ||||||
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 / Resolution: 1.71 Å | ||||||
Authors | Shoichet, B.K. / Barelier, S. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2014 Title: Substrate deconstruction and the nonadditivity of enzyme recognition. Authors: Barelier, S. / Cummings, J.A. / Rauwerdink, A.M. / Hitchcock, D.S. / Farelli, J.D. / Almo, S.C. / Raushel, F.M. / Allen, K.N. / 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 | 4olg.cif.gz | 155.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4olg.ent.gz | 128.9 KB | Display | PDB format |
PDBx/mmJSON format | 4olg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ol/4olg ftp://data.pdbj.org/pub/pdb/validation_reports/ol/4olg | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 39587.922 Da / Num. of mol.: 2 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 | #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: 2.55 Å3/Da / Density % sol: 51.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.6 Details: 1.7 M POTASSIUM PHOSPHATE, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115869 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 11, 2012 |
Radiation | Monochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.115869 Å / Relative weight: 1 |
Reflection | Resolution: 1.71→30 Å / Num. all: 85920 / Num. obs: 85387 / % possible obs: 99.4 % / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 1.71→1.81 Å / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.71→29.41 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.845 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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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 max: 107.28 Å2 / Biso mean: 28.513 Å2 / Biso min: 15.03 Å2
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Refinement step | Cycle: LAST / Resolution: 1.71→29.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.711→1.756 Å / Total num. of bins used: 20
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