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- PDB-1n9b: Ultrahigh resolution structure of a class A beta-lactamase: On th... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1n9b | ||||||
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Title | Ultrahigh resolution structure of a class A beta-lactamase: On the mechanism and specificity of the extended-spectrum SHV-2 enzyme | ||||||
![]() | BETA-LACTAMASE SHV-2 | ||||||
![]() | HYDROLASE / BETA-LACTAM HYDROLASE / PENICILLINASE / DETERGENT BINDING / DRUG DESIGN / RADIATION DAMAGE | ||||||
Function / homology | ![]() beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nukaga, M. / Mayama, K. / Hujer, A.M. / Bonomo, R.A. / Knox, J.R. | ||||||
![]() | ![]() Title: Ultrahigh resolution structure of a class A beta-lactamase: On the mechanism and specificity of the extended-spectrum SHV-2 enzyme Authors: Nukaga, M. / Mayama, K. / Hujer, A.M. / 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 | ![]() | 142.7 KB | Display | ![]() |
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PDB format | ![]() | 110.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 17.5 KB | Display | |
Data in CIF | ![]() | 27.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1shvS 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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Unit cell |
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Components
#1: Protein | Mass: 28937.045 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() Strain (production host): DH10B / References: UniProt: P30896, beta-lactamase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-EPE / | #4: Chemical | ChemComp-MPD / ( | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: PEG 6000, HEPES, CYMAL-6, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 38 % | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||
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 4 / Detector: CCD / Date: Mar 24, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.948 Å / Relative weight: 1 |
Reflection | Resolution: 0.9→50 Å / Num. all: 164255 / Num. obs: 164255 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 0.9→0.95 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 18796 / Rsym value: 0.5 / % possible all: 74.2 |
Reflection | *PLUS Highest resolution: 0.9 Å / Lowest resolution: 50 Å / Num. obs: 161543 / % possible obs: 97 % / Num. measured all: 827345 / Rmerge(I) obs: 0.081 |
Reflection shell | *PLUS Highest resolution: 0.91 Å / Lowest resolution: 0.96 Å / % possible obs: 84.7 % / Num. unique obs: 20721 / Num. measured obs: 55094 / Rmerge(I) obs: 0.526 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1SHV Resolution: 0.9→10 Å / Num. parameters: 24004 / Num. restraintsaints: 237532 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: Hydrogen atoms included in refinement but not deposited; Anisotropic refinement. Coordinate error estimated from a full-matrix LS cycle is 0.020 angstroms.
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Displacement parameters | Biso mean: 14.5 Å2 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 88 / Occupancy sum hydrogen: 2020.18 / Occupancy sum non hydrogen: 2391.85 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.9→10 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 10 Å / Num. reflection obs: 155457 / % reflection Rfree: 5 % / Rfactor Rfree: 0.15 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |