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Yorodumi- PDB-7e9a: Crystal structure of KPC-2 in complex with (S)-2-(1-hydroxy-1,3-d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7e9a | ||||||||||||
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Title | Crystal structure of KPC-2 in complex with (S)-2-(1-hydroxy-1,3-dihydrobenzo[c][1,2]oxaborol-3-yl)acrylic acid (4a-(S)) | ||||||||||||
Components | Beta-lactamase | ||||||||||||
Keywords | HYDROLASE / Beta-lactamase / Serine-beta-lactamase KPC-2 / KPC-2 / Carbapenemase | ||||||||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||||||||
Biological species | Klebsiella pneumoniae (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å | ||||||||||||
Authors | Li, G.-B. / Yan, Y.-H. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: Chem.Commun.(Camb.) / Year: 2021 Title: Design and enantioselective synthesis of 3-( alpha-acrylic acid) benzoxaboroles to combat carbapenemase resistance. Authors: Xiao, Y.C. / Chen, X.P. / Deng, J. / Yan, Y.H. / Zhu, K.R. / Li, G. / Yu, J.L. / Brem, J. / Chen, F. / Schofield, C.J. / Li, G.B. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7e9a.cif.gz | 218 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7e9a.ent.gz | 173.6 KB | Display | PDB format |
PDBx/mmJSON format | 7e9a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7e9a_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 7e9a_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 7e9a_validation.xml.gz | 44.9 KB | Display | |
Data in CIF | 7e9a_validation.cif.gz | 61.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e9/7e9a ftp://data.pdbj.org/pub/pdb/validation_reports/e9/7e9a | HTTPS FTP |
-Related structure data
Related structure data | 6jn3S S: Starting model for refinement |
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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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3 |
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4 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 28079.584 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Klebsiella pneumoniae / Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaKPC2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q93LQ9, beta-lactamase |
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-Non-polymers , 5 types, 391 molecules
#2: Chemical | ChemComp-J00 / #3: Chemical | #4: Chemical | ChemComp-PEG / #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
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-Details
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: 3.34 Å3/Da / Density % sol: 63.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 32-35% PEG 8000, 0.1M lithium sulphate, 0.05M sodium acetate (pH 4.5) |
-Data collection
Diffraction | Mean temperature: 195 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 X CdTe 1M / Detector: PIXEL / Date: Dec 24, 2018 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.25→50 Å / Num. obs: 70988 / % possible obs: 100 % / Redundancy: 19.9 % / Biso Wilson estimate: 30.48 Å2 / Rmerge(I) obs: 0.239 / Rpim(I) all: 0.055 / Rrim(I) all: 0.245 / Χ2: 1.059 / Net I/σ(I): 3.6 / Num. measured all: 1412966 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 100
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6JN3 Resolution: 2.25→47.43 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.97 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 175.36 Å2 / Biso mean: 34.8114 Å2 / Biso min: 10.42 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.25→47.43 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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