+Open data
-Basic information
Entry | Database: PDB / ID: 5qao | ||||||
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Title | OXA-48 IN COMPLEX WITH COMPOUND 19b | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / Oxacillinase / Inhibitor / Complex / OXA / Antibiotic resistance / beta-lactamase / fragment | ||||||
Function / homology | Function and homology information penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic / metal ion binding Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Lund, B.A. / Leiros, H.K.S. | ||||||
Citation | Journal: Eur J Med Chem / Year: 2018 Title: A focused fragment library targeting the antibiotic resistance enzyme - Oxacillinase-48: Synthesis, structural evaluation and inhibitor design. Authors: Akhter, S. / Lund, B.A. / Ismael, A. / Langer, M. / Isaksson, J. / Christopeit, T. / Leiros, H.S. / Bayer, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5qao.cif.gz | 585.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5qao.ent.gz | 494.3 KB | Display | PDB format |
PDBx/mmJSON format | 5qao.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5qao_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 5qao_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 5qao_validation.xml.gz | 44 KB | Display | |
Data in CIF | 5qao_validation.cif.gz | 61.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qa/5qao ftp://data.pdbj.org/pub/pdb/validation_reports/qa/5qao | HTTPS FTP |
-Group deposition
ID | G_1002027 (37 entries) |
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Title | A focused fragment library targeting the antibiotic resistance enzyme - oxacillinase-48: synthesis, structural evaluation and inhibitor design |
Type | undefined |
Description | A focused fragment library targeting the antibiotic resistance enzyme - oxacillinase-48: synthesis, structural evaluation and inhibitor design |
-Related structure data
Related structure data | 5dtkS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: PRO / End label comp-ID: PRO / Auth seq-ID: 24 - 265 / Label seq-ID: 2 - 243
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 28226.951 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla OXA-48, blaOXA-48, KPE71T_00045 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6XEC0, beta-lactamase |
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-Non-polymers , 5 types, 745 molecules
#2: Chemical | ChemComp-Z8R / #3: Chemical | #4: Chemical | ChemComp-DMS / | #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: 2.64 Å3/Da / Density % sol: 53.45 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M HEPES pH 7.5, 8-11% PEG 8000 and 4-8% 1-butanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.98401 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98401 Å / Relative weight: 1 |
Reflection | Resolution: 2→62.66 Å / % possible obs: 96.78 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.1512 / Rrim(I) all: 0.17 / Net I/σ(I): 3.8 |
Reflection shell | Resolution: 2→2.07 Å / % possible obs: 98.7 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.5944 / Num. unique obs: 34116 / Rrim(I) all: 0.67 / Net I/σ(I) obs: 1.64 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY: 5dtk Resolution: 2→62.66 Å / Cross valid method: THROUGHOUT
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Refinement step | Cycle: final / Resolution: 2→62.66 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28
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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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