+Open data
-Basic information
Entry | Database: PDB / ID: 7t7e | ||||||
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Title | MA-1-206-OXA-23 3 minute complex | ||||||
Components | Beta-lactamase OXA-23 | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / antibiotic resistance / inhibitor / complex / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / penicillin binding / cell wall organization / Beta-lactamase/transpeptidase-like / Chem-FDX / OXA-23 Function and homology information | ||||||
Biological species | Acinetobacter baumannii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Smith, C.A. / Stewart, N.K. / Vakulenko, S.B. | ||||||
Funding support | United States, 1items
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Citation | Journal: Mbio / Year: 2022 Title: C6 Hydroxymethyl-Substituted Carbapenem MA-1-206 Inhibits the Major Acinetobacter baumannii Carbapenemase OXA-23 by Impeding Deacylation. Authors: Stewart, N.K. / Toth, M. / Alqurafi, M.A. / Chai, W. / Nguyen, T.Q. / Quan, P. / Lee, M. / Buynak, J.D. / Smith, C.A. / Vakulenko, S.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7t7e.cif.gz | 114.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7t7e.ent.gz | 87.2 KB | Display | PDB format |
PDBx/mmJSON format | 7t7e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7t7e_validation.pdf.gz | 786.3 KB | Display | wwPDB validaton report |
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Full document | 7t7e_full_validation.pdf.gz | 789.4 KB | Display | |
Data in XML | 7t7e_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | 7t7e_validation.cif.gz | 15 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t7/7t7e ftp://data.pdbj.org/pub/pdb/validation_reports/t7/7t7e | HTTPS FTP |
-Related structure data
Related structure data | 7t7dC 7t7fC 7t7gC 4jf6S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 27689.936 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: V5TGX0 |
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#2: Chemical | ChemComp-FDX / ( |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.57 Å3/Da / Density % sol: 77.91 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.2 M succinic acid, 20% PEG3350 |
-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: 0.97949 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→39 Å / Num. obs: 24682 / % possible obs: 99.9 % / Redundancy: 8.8 % / CC1/2: 0.999 / Rpim(I) all: 0.021 / Rrim(I) all: 0.064 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 8.8 % / Mean I/σ(I) obs: 2 / Num. unique obs: 2532 / CC1/2: 0.893 / Rpim(I) all: 0.318 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4JF6 Resolution: 2.4→38.97 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 32.74 / 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: 145.36 Å2 / Biso mean: 78.0539 Å2 / Biso min: 48.31 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.4→38.97 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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