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- PDB-1kvl: X-ray Crystal Structure of AmpC S64G Mutant beta-Lactamase in Com... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1kvl | ||||||
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Title | X-ray Crystal Structure of AmpC S64G Mutant beta-Lactamase in Complex with Substrate and Product Forms of Cephalothin | ||||||
![]() | Beta-lactamase | ||||||
![]() | HYDROLASE / amide hydrolase / beta-lactamase / cephalothin / substrate-enzyme complex / product-enzyme complex | ||||||
Function / homology | ![]() antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Beadle, B.M. / Trehan, I. / Focia, P.J. / Shoichet, B.K. | ||||||
![]() | ![]() Title: Structural milestones in the reaction pathway of an amide hydrolase: substrate, acyl, and product complexes of cephalothin with AmpC beta-lactamase. Authors: Beadle, B.M. / Trehan, I. / Focia, P.J. / Shoichet, B.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 164.2 KB | Display | ![]() |
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PDB format | ![]() | 127.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1kvmC ![]() 1c3bS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 39557.895 Da / Num. of mol.: 2 / Mutation: S64G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 493 molecules ![](data/chem/img/PO4.gif)
![](data/chem/img/KCP.gif)
![](data/chem/img/CLS.gif)
![](data/chem/img/THN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/KCP.gif)
![](data/chem/img/CLS.gif)
![](data/chem/img/THN.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-KCP / | #4: Chemical | ChemComp-CLS / | #5: Chemical | ChemComp-THN / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.79 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.7 Details: 1.7 M potassium phosphate; the crystal was then soaked in saturated cephalothin in crystallizing buffer for 3 hours, 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 / Details: pH8.7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 11, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→20 Å / Num. obs: 108082 / % possible obs: 90.3 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 28.2 |
Reflection shell | Resolution: 1.53→1.57 Å / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.14 / % possible all: 95.5 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 385475 |
Reflection shell | *PLUS % possible obs: 95.5 % / Rmerge(I) obs: 0.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1C3B Resolution: 1.53→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | ksol: 0.383662 e/Å3 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.1656 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.53→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.53→1.58 Å
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Xplor file |
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Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 2.5 % / Rfactor obs: 0.195 / Rfactor Rfree: 0.22 | ||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 1.57 Å |