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Yorodumi- PDB-1i5q: CRYSTAL STRUCTURE OF THE E. COLI AMPC BETA-LACTAMASE MUTANT N152A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1i5q | ||||||
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Title | CRYSTAL STRUCTURE OF THE E. COLI AMPC BETA-LACTAMASE MUTANT N152A COVALENTLY ACYLATED WITH THE INHIBITORY BETA-LACTAM, MOXALACTAM | ||||||
Components | BETA-LACTAMASE | ||||||
Keywords | HYDROLASE / cephalosporinase / beta-lactamase / serine hydrolase | ||||||
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: 1.83 Å | ||||||
Authors | Trehan, I. / Beadle, B.M. / Shoichet, B.K. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Inhibition of AmpC beta-lactamase through a destabilizing interaction in the active site. Authors: Trehan, I. / Beadle, B.M. / 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 | 1i5q.cif.gz | 158 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i5q.ent.gz | 124.5 KB | Display | PDB format |
PDBx/mmJSON format | 1i5q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i5/1i5q ftp://data.pdbj.org/pub/pdb/validation_reports/i5/1i5q | HTTPS FTP |
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-Related structure data
Related structure data | 1c3bS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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 / Mutation: N152A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: AMPC / Plasmid: POGO295 / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K12 / References: UniProt: P00811, beta-lactamase #2: Chemical | #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: 2.5 Å3/Da / Density % sol: 50.9 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.7 Details: potassium phosphate, AmpC N152A, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
Crystal grow | *PLUS Temperature: 23 ℃ |
Components of the solutions | *PLUS Conc.: 1.7 M / Common name: potassium phosphate |
-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: Aug 20, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→20 Å / Num. all: 68795 / Num. obs: 274720 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.99 % / Biso Wilson estimate: 21.732 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 22.08 |
Reflection shell | Resolution: 1.83→1.87 Å / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 1.69 / Num. unique all: 4551 / % possible all: 99.9 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 68795 / Num. measured all: 274720 |
Reflection shell | *PLUS % possible obs: 99.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 1C3B with inhibitor, solvent, and N152 sidechain atoms (beyond C-beta) removed Resolution: 1.83→20 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.83→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.83→1.87 Å / Total num. of bins used: 15 /
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Xplor file | Serial no: 1 / Param file: moxalactam.par / Topol file: moxalactam.top | |||||||||||||||||||||||||
Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 3 % / Rfactor obs: 0.168 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_bond_d / Dev ideal: 0.0139 |