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Open data
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Basic information
Entry | Database: PDB / ID: 1onh | ||||||
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Title | GC1 beta-lactamase with a penem inhibitor | ||||||
![]() | class C beta-lactamase | ||||||
![]() | HYDROLASE / MIXED ALPHA/BETA / CEPHALOSPORINASE / INHIBITION / CLASS C BETA-LACTAMASE | ||||||
Function / homology | ![]() antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nukaga, M. / Nukaga, K. / Knox, J.R. | ||||||
![]() | ![]() Title: Inhibition of Class A and Class C Beta-Lactamases by Penems: Crystallographic Structures of a Novel 1,4-Thiazepine Intermediate Authors: Nukaga, M. / Abe, T. / Venkatesan, A.M. / Mansour, T.S. / Bonomo, R.A. / Knox, J.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 176.4 KB | Display | ![]() |
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PDB format | ![]() | 139.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 830.6 KB | Display | ![]() |
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Full document | ![]() | 836.5 KB | Display | |
Data in XML | ![]() | 20.3 KB | Display | |
Data in CIF | ![]() | 31.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ongC ![]() 1gceS S: Starting model for refinement C: citing same article ( |
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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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 39609.172 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-WY4 / | ||
#3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 10% PEG 8000 in 50 mM HEPES over 20 % PEG, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 24, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9474 Å / Relative weight: 1 |
Reflection | Resolution: 1.38→50 Å / Num. obs: 65047 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 1.38→1.43 Å / Redundancy: 2.52 % / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 2 / Num. unique all: 5075 / % possible all: 77 |
Reflection | *PLUS Highest resolution: 1.38 Å / Num. measured all: 377696 |
Reflection shell | *PLUS % possible obs: 77 % / Num. unique obs: 5075 / Num. measured obs: 12765 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1GCE Resolution: 1.38→20 Å / Num. parameters: 30398 / Num. restraintsaints: 38104 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze | Num. disordered residues: 36 / Occupancy sum hydrogen: 2680.96 / Occupancy sum non hydrogen: 3219.6 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.38→20 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / Rfactor Rfree: 0.202 / Rfactor Rwork: 0.138 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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