+Open data
-Basic information
Entry | Database: PDB / ID: 7peh | ||||||
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Title | Crystal Structure of a Class D Carbapenemase | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / OXA / apo | ||||||
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: 1.92 Å | ||||||
Authors | Zhou, Q. / He, Y. / Jin, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: Acs Cent.Sci. / Year: 2023 Title: An Ion-Pair Induced Intermediate Complex Captured in Class D Carbapenemase Reveals Chloride Ion as a Janus Effector Modulating Activity Authors: Zhou, Q. / Catalan, P. / Bell, H. / Baumann, P. / Cooke, R. / Evans, R. / Yang, J. / Zhang, Z. / Zappala, D. / Zhang, Y. / Blackburn, G.M. / He, Y. / Jin, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7peh.cif.gz | 397 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7peh.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7peh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pe/7peh ftp://data.pdbj.org/pub/pdb/validation_reports/pe/7peh | HTTPS FTP |
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-Related structure data
Related structure data | 7nrjC 7o5nC 7o5tC 7o9nC 7peiC 7pepC 7pfnC 7pgoC 7pseC 7psfC 7q14C 4s2pS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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 / 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: 19 - 260
NCS ensembles :
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-Components
#1: Protein | Mass: 30254.133 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) Gene: bla OXA-48, bla_2, blaOXA-48, G5637_27540, KPE71T_00045, SAMEA3649466_05396 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6XEC0, beta-lactamase #2: Chemical | ChemComp-1BO / #3: Water | ChemComp-HOH / | 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: 2.29 Å3/Da / Density % sol: 46.19 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES pH 7.5, 11.6% PEG8000, 8% 1-BuOH, mixed with the 10 mg/mL protein stock at 1:1 ratio. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.815342 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 24, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.815342 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→53.84 Å / Num. obs: 85231 / % possible obs: 99.9 % / Redundancy: 12 % / CC1/2: 0.994 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 1.92→1.96 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 4431 / CC1/2: 0.588 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4S2P Resolution: 1.92→53.84 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.928 / SU B: 5.923 / SU ML: 0.153 / Cross valid method: FREE R-VALUE / ESU R: 0.181 / ESU R Free: 0.158 Details: Hydrogens have been added in their 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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.047 Å2
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Refinement step | Cycle: LAST / Resolution: 1.92→53.84 Å
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Refine LS restraints |
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