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Yorodumi- PDB-1pi5: Structure of N289A mutant of AmpC in complex with SM2, carboxyphe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pi5 | ||||||
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Title | Structure of N289A mutant of AmpC in complex with SM2, carboxyphenylglycylboronic acid bearing the cephalothin R1 side chain | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / Enzyme Inhibitor Complex / Beta-Lactamase | ||||||
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: 1.49 Å | ||||||
Authors | Roth, T.A. / Minasov, G. / Focia, P.J. / Shoichet, B.K. | ||||||
Citation | Journal: Biochemistry / Year: 2003 Title: Thermodynamic cycle analysis and inhibitor design against beta-lactamase. Authors: Roth, T.A. / Minasov, G. / Morandi, S. / Prati, F. / 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 | 1pi5.cif.gz | 192.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pi5.ent.gz | 152.8 KB | Display | PDB format |
PDBx/mmJSON format | 1pi5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pi/1pi5 ftp://data.pdbj.org/pub/pdb/validation_reports/pi/1pi5 | HTTPS FTP |
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-Related structure data
Related structure data | 1pi4C 1mxoS S: Starting model for refinement C: citing same article (ref.) |
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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: 39544.898 Da / Num. of mol.: 2 / Fragment: AmpC / Mutation: N289A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: AMPC OR AMPA OR B4150 / Plasmid: POGO295 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00811, beta-lactamase #2: Chemical | ChemComp-PO4 / | #3: Chemical | #4: Chemical | #5: 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: 1.91 Å3/Da / Density % sol: 35.05 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.7 Details: Potassium Phosphate Buffer , pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 1, 2002 / Details: Mirrors |
Radiation | Monochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→15 Å / Num. all: 128092 / Num. obs: 128092 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 23.8 |
Reflection shell | Resolution: 1.49→1.54 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.184 / Mean I/σ(I) obs: 7.6 / Num. unique all: 12767 / % possible all: 100 |
Reflection | *PLUS Num. measured all: 483237 |
Reflection shell | *PLUS % possible obs: 100 % / Num. unique obs: 12767 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1MXO Resolution: 1.49→15 Å Isotropic thermal model: Isotropic with refined individual B-factors Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Maximum Likelihood in the refinement
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Solvent computation | Bsol: 250 Å2 / ksol: 0.647 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.49→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.49→1.54 Å
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Refinement | *PLUS Rfactor Rwork: 0.156 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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