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Yorodumi- PDB-7o0o: Crystal structure of the B3 metallo-beta-lactamase L1 with hydrol... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7o0o | |||||||||
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Title | Crystal structure of the B3 metallo-beta-lactamase L1 with hydrolysed ertapenem | |||||||||
Components | Metallo-beta-lactamase L1 | |||||||||
Keywords | ANTIMICROBIAL PROTEIN / antibiotic / ligand / metalloprotein / lactamase / carbapenem | |||||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding Similarity search - Function | |||||||||
Biological species | Stenotrophomonas maltophilia (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | |||||||||
Authors | Hinchliffe, P. / Spencer, J. | |||||||||
Funding support | United States, 1items
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Citation | Journal: J.Chem.Inf.Model. / Year: 2021 Title: Crystallography and QM/MM Simulations Identify Preferential Binding of Hydrolyzed Carbapenem and Penem Antibiotics to the L1 Metallo-beta-Lactamase in the Imine Form. Authors: Twidale, R.M. / Hinchliffe, P. / Spencer, J. / Mulholland, A.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7o0o.cif.gz | 171 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7o0o.ent.gz | 136.4 KB | Display | PDB format |
PDBx/mmJSON format | 7o0o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7o0o_validation.pdf.gz | 733.1 KB | Display | wwPDB validaton report |
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Full document | 7o0o_full_validation.pdf.gz | 736.4 KB | Display | |
Data in XML | 7o0o_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | 7o0o_validation.cif.gz | 23.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o0/7o0o ftp://data.pdbj.org/pub/pdb/validation_reports/o0/7o0o | HTTPS FTP |
-Related structure data
Related structure data | 5evdS S: Starting model for refinement |
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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
#1: Protein | Mass: 28894.619 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Stenotrophomonas maltophilia (bacteria) Production host: Escherichia coli (E. coli) / References: UniProt: P52700, beta-lactamase | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-9XS / ( | #4: Chemical | #5: 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: 2.74 Å3/Da / Density % sol: 55.18 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 100 mM Hepes pH 7.75, 2.0 M ammonium sulphate, 1.5% PEG400. 1 ul protein (15 mg/ml) mixed with 1 ul reservoir. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96862 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 15, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96862 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→46.57 Å / Num. obs: 57760 / % possible obs: 100 % / Redundancy: 36.7 % / CC1/2: 0.999 / Rpim(I) all: 0.024 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 1.45→1.47 Å / Redundancy: 30.3 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2805 / CC1/2: 0.804 / Rpim(I) all: 0.54 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5EVD Resolution: 1.45→32.72 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 17.65 / 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: 135.29 Å2 / Biso mean: 28.3419 Å2 / Biso min: 11.53 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.45→32.72 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20
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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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