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Yorodumi- PDB-7mef: CDD-1 beta-lactamase in imidazole/MPD 10 minute avibactam complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 7mef | ||||||
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Title | CDD-1 beta-lactamase in imidazole/MPD 10 minute avibactam complex | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE/INHIBITOR / Gram-positive / beta-lactamase / antibiotic resistance / inhibitor / avibactam / HYDROLASE / HYDROLASE-INHIBITOR complex | ||||||
Function / homology | Function and homology information penicillin binding / antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / membrane Similarity search - Function | ||||||
Biological species | Clostridioides difficile (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å | ||||||
Authors | Smith, C.A. / Vakulenko, S.B. | ||||||
Citation | Journal: Acs Infect Dis. / Year: 2021 Title: In Crystallo Time-Resolved Interaction of the Clostridioides difficile CDD-1 enzyme with Avibactam Provides New Insights into the Catalytic Mechanism of Class D beta-lactamases. Authors: Stewart, N.K. / Toth, M. / Stasyuk, A. / Vakulenko, S.B. / Smith, C.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7mef.cif.gz | 67 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7mef.ent.gz | 51.9 KB | Display | PDB format |
PDBx/mmJSON format | 7mef.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7mef_validation.pdf.gz | 983.6 KB | Display | wwPDB validaton report |
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Full document | 7mef_full_validation.pdf.gz | 984.6 KB | Display | |
Data in XML | 7mef_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 7mef_validation.cif.gz | 19 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/me/7mef ftp://data.pdbj.org/pub/pdb/validation_reports/me/7mef | HTTPS FTP |
-Related structure data
Related structure data | 7lnoC 7lnqC 7lnrC 7me9C 7meaC 7mebC 7mecC 7medC 7meeC 7megC 7mehC C: citing same article (ref.) |
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Similar structure data |
-Links
-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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 28574.234 Da / Num. of mol.: 1 / Mutation: K238A, K244A Source method: isolated from a genetically manipulated source Details: double lysine to alanine mutant Lys238Ala and Lys244Ala Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: blaR1_1, E5F32_07085, E5F39_11445, SAMEA3374989_01677 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A160YKM3, beta-lactamase |
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-Non-polymers , 5 types, 163 molecules
#2: Chemical | ChemComp-NXL / ( | ||||
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#3: Chemical | ChemComp-CO2 / | ||||
#4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-MPD / ( | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 2.77 Å3/Da / Density % sol: 55.55 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 7.0, 2.4 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 1, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→39.2 Å / Num. obs: 26101 / % possible obs: 99.9 % / Redundancy: 16.9 % / CC1/2: 0.998 / Rpim(I) all: 0.032 / Rrim(I) all: 0.13 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.9→1.95 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1701 / CC1/2: 0.776 / Rpim(I) all: 0.378 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.9→39.15 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.16 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 86.74 Å2 / Biso mean: 37.3179 Å2 / Biso min: 19.07 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→39.15 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9
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