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Yorodumi- PDB-6t35: Crystal structure of AmpC from E.coli with Enmetazobactam (AAI-101) -
+Open data
-Basic information
Entry | Database: PDB / ID: 6t35 | |||||||||
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Title | Crystal structure of AmpC from E.coli with Enmetazobactam (AAI-101) | |||||||||
Components | Beta-lactamase | |||||||||
Keywords | HYDROLASE / beta lactamase / antibiotic resistance / antimicrobial protein / mechanism based inhibitor | |||||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic Similarity search - Function | |||||||||
Biological species | Escherichia coli K-12 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å | |||||||||
Authors | Lang, P.A. / Leissing, T.M. / Schofield, C.J. / Brem, J. | |||||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2022 Title: Studies on enmetazobactam clarify mechanisms of widely used beta-lactamase inhibitors. Authors: Lang, P.A. / Raj, R. / Tumber, A. / Lohans, C.T. / Rabe, P. / Robinson, C.V. / Brem, J. / Schofield, C.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6t35.cif.gz | 161.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6t35.ent.gz | 124.3 KB | Display | PDB format |
PDBx/mmJSON format | 6t35.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6t35_validation.pdf.gz | 751.4 KB | Display | wwPDB validaton report |
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Full document | 6t35_full_validation.pdf.gz | 752.5 KB | Display | |
Data in XML | 6t35_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 6t35_validation.cif.gz | 25.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t3/6t35 ftp://data.pdbj.org/pub/pdb/validation_reports/t3/6t35 | HTTPS FTP |
-Related structure data
Related structure data | 7b3rC 7b3sC 7b3uC 1iemS S: Starting model for refinement 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: 39587.922 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: ampC, ampA, b4150, JW4111 Production host: Escherichia coli str. K-12 substr. W3110 (bacteria) References: UniProt: P00811, beta-lactamase |
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-Non-polymers , 6 types, 264 molecules
#2: Chemical | ChemComp-SO4 / | ||||||||
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#3: Chemical | #4: Chemical | ChemComp-M9W / | #5: Chemical | #6: Chemical | ChemComp-CL / | #7: 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: 55.53 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 30% w/v PEG6000, 0.01 M ZnCl2, 0.1 M MES pH = 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 1, 2018 / Details: mirror | ||||||||||||||||||||||||||||||
Radiation | Monochromator: Double mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.75→56.34 Å / Num. obs: 45784 / % possible obs: 100 % / Redundancy: 77.5 % / CC1/2: 1 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.015 / Rrim(I) all: 0.129 / Net I/σ(I): 28.1 / Num. measured all: 3549347 / Scaling rejects: 1 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1IEM Resolution: 1.75→43.639 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.4
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 106.84 Å2 / Biso mean: 39.078 Å2 / Biso min: 22.41 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.75→43.639 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % 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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