+Open data
-Basic information
Entry | Database: PDB / ID: 6n6u | ||||||
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Title | OXA-23 mutant F110A/M221A low pH form imipenem complex | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / carbapenemase / antibiotic resistance / mutant | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Acinetobacter baumannii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Smith, C.A. / Vakulenko, S.B. | ||||||
Citation | Journal: Antimicrob. Agents Chemother. / Year: 2019 Title: Role of the Hydrophobic Bridge in the Carbapenemase Activity of Class D beta-Lactamases. Authors: Stewart, N.K. / Smith, C.A. / Antunes, N.T. / Toth, M. / 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 | 6n6u.cif.gz | 114.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6n6u.ent.gz | 86.5 KB | Display | PDB format |
PDBx/mmJSON format | 6n6u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n6/6n6u ftp://data.pdbj.org/pub/pdb/validation_reports/n6/6n6u | HTTPS FTP |
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-Related structure data
Related structure data | 6n6tC 6n6vC 6n6wC 6n6xC 6n6yC 4jf5S 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
#1: Protein | Mass: 27453.670 Da / Num. of mol.: 1 / Fragment: UNP residues 32-273 / Mutation: F110A/M221A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) Gene: ari-1, bla(OXA-23), bla-OXA-23, bla-oxa-23, bla_1, bla_2, bla_3, blaOXA, blaOXA-23, blaOXA23, OXA-23, oxa-23, oxa23, A7M90_19440, AB719_18095, ABUW_0563, AZE33_05050, AZE33_05100, AZE33_05150, ...Gene: ari-1, bla(OXA-23), bla-OXA-23, bla-oxa-23, bla_1, bla_2, bla_3, blaOXA, blaOXA-23, blaOXA23, OXA-23, oxa-23, oxa23, A7M90_19440, AB719_18095, ABUW_0563, AZE33_05050, AZE33_05100, AZE33_05150, AZE33_05250, C7G90_19950, CAS83_19595, CBE85_20255, CBI29_04474, CEJ63_03230, DV997_16620, DVA79_19285, IX87_16825, IX87_21860, LV38_03424, NG19_0098, SAMEA104305208_04008, SAMEA104305229_06308, SAMEA104305235_03908, SAMEA104305242_04084, SAMEA104305268_03570, SAMEA104305271_04290, SAMEA104305299_06196, SAMEA104305318_04148, SAMEA104305320_04271, SAMEA104305325_04185, SAMEA104305341_03854, SAMEA104305343_03919, SAMEA104305351_03822, SAMEA104305385_00775 Production host: Escherichia coli (E. coli) / References: UniProt: Q9L4P2, beta-lactamase |
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#2: Chemical | ChemComp-ID1 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.1 Details: 0.06 M citric acid, 0.04 M bis-Tris propane, pH 4.1, 16% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 19, 2018 |
Radiation | Monochromator: Liquid nitrogen-cooled double crystal Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→38.2 Å / Num. obs: 41612 / % possible obs: 99.8 % / Redundancy: 7.2 % / Rpim(I) all: 0.023 / Rrim(I) all: 0.062 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.55→1.58 Å / Num. unique obs: 1995 / Rpim(I) all: 0.359 / Rrim(I) all: 0.947 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4JF5 Resolution: 1.55→37.072 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.47
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 67.49 Å2 / Biso mean: 24.2855 Å2 / Biso min: 8.47 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.55→37.072 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15
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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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