+Open data
-Basic information
Entry | Database: PDB / ID: 4s2p | ||||||
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Title | Crystal structure of unbound OXA-48 | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE | ||||||
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: 1.7 Å | ||||||
Authors | King, D.T. / Strynadka, N.C.J. | ||||||
Citation | Journal: ACS Infect Dis / Year: 2015 Title: Molecular Mechanism of Avibactam-Mediated beta-Lactamase Inhibition. Authors: King, D.T. / King, A.M. / Lal, S.M. / Wright, G.D. / Strynadka, N.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4s2p.cif.gz | 112.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4s2p.ent.gz | 92.8 KB | Display | PDB format |
PDBx/mmJSON format | 4s2p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4s2p_validation.pdf.gz | 445.2 KB | Display | wwPDB validaton report |
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Full document | 4s2p_full_validation.pdf.gz | 454.9 KB | Display | |
Data in XML | 4s2p_validation.xml.gz | 23.7 KB | Display | |
Data in CIF | 4s2p_validation.cif.gz | 34 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s2/4s2p ftp://data.pdbj.org/pub/pdb/validation_reports/s2/4s2p | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Details | This protein behaves as a dimer in solution |
-Components
#1: Protein | Mass: 30439.725 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla OXA-48, blaOXA-48, FP68_27275, KPE71T_00045 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6XEC0, beta-lactamase #2: 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: 2.29 Å3/Da / Density % sol: 46.22 % |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 200mM tris pH 7.5, 0.1M ammonium chloride, 40% MPD, 5% PEG 8K, 100 mM NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 298.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Jun 13, 2013 |
Radiation | Monochromator: double crystal monochromator (DCM) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→41.6 Å / Num. all: 62413 / Num. obs: 62226 / % possible obs: 99.7 % |
Reflection shell | Resolution: 1.7→1.73 Å / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→41.6 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.669 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.524 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→41.6 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 15864 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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