+Open data
-Basic information
Entry | Database: PDB / ID: 5mox | ||||||
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Title | OXA-10 Avibactam complex with bound CO2 | ||||||
Components | Beta-lactamase OXA-10 | ||||||
Keywords | HYDROLASE / antibiotic resistance | ||||||
Function / homology | Function and homology information penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.41 Å | ||||||
Authors | Brem, J. | ||||||
Citation | Journal: Org. Biomol. Chem. / Year: 2017 Title: (13)C-Carbamylation as a mechanistic probe for the inhibition of class D beta-lactamases by avibactam and halide ions. Authors: Lohans, C.T. / Wang, D.Y. / Jorgensen, C. / Cahill, S.T. / Clifton, I.J. / McDonough, M.A. / Oswin, H.P. / Spencer, J. / Domene, C. / Claridge, T.D.W. / 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 | 5mox.cif.gz | 220.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mox.ent.gz | 174.2 KB | Display | PDB format |
PDBx/mmJSON format | 5mox.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mox_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5mox_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5mox_validation.xml.gz | 27.2 KB | Display | |
Data in CIF | 5mox_validation.cif.gz | 41 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mo/5mox ftp://data.pdbj.org/pub/pdb/validation_reports/mo/5mox | HTTPS FTP |
-Related structure data
Related structure data | 5mmyC 5mnuC 5mozC 5fq9S 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 27655.488 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: bla, oxa10, pse2 / Production host: Escherichia coli (E. coli) / References: UniProt: P14489, beta-lactamase |
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-Non-polymers , 5 types, 619 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CO2 / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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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: 3.2 Å3/Da / Density % sol: 61 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2M Sodium citrate tribasic dihydrate, 0.1M Bis-Tris propane 7.5, 20 % w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 26, 2016 / Details: mirror |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.41→76.76 Å / Num. obs: 115816 / % possible obs: 100 % / Observed criterion σ(I): 1.2 / Redundancy: 12.9 % / Rmerge(I) obs: 0.179 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.41→1.43 Å / Redundancy: 12.6 % / Rmerge(I) obs: 3.083 / Mean I/σ(I) obs: 1.2 / Num. unique all: 5742 / CC1/2: 0.511 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5FQ9 Resolution: 1.41→76.76 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso max: 90.63 Å2 / Biso mean: 19.0961 Å2 / Biso min: 5.54 Å2 | ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.41→76.76 Å
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