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Yorodumi- PDB-6z25: Acylenzyme complex of ceftazidime bound to deacylation mutant KPC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6z25 | |||||||||
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Title | Acylenzyme complex of ceftazidime bound to deacylation mutant KPC-4 (E166Q) | |||||||||
Components | Beta-lactamase | |||||||||
Keywords | ANTIMICROBIAL PROTEIN / unliganded beta-lactamase / 3-layer alpha-beta-alpha sandwich / part of the DD-peptidase and beta-lactamase superfamily. | |||||||||
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 / Resolution: 1.24 Å | |||||||||
Authors | Tooke, C.L. / Hinchliffe, P. / Spencer, J. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: J.Biol.Chem. / Year: 2020 Title: Natural variants modify Klebsiella pneumoniae carbapenemase (KPC) acyl-enzyme conformational dynamics to extend antibiotic resistance. Authors: Tooke, C.L. / Hinchliffe, P. / Bonomo, R.A. / Schofield, C.J. / Mulholland, A.J. / Spencer, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6z25.cif.gz | 182.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6z25.ent.gz | 147.3 KB | Display | PDB format |
PDBx/mmJSON format | 6z25.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6z25_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6z25_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6z25_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 6z25_validation.cif.gz | 22.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z2/6z25 ftp://data.pdbj.org/pub/pdb/validation_reports/z2/6z25 | HTTPS FTP |
-Related structure data
Related structure data | 6z21C 6z22C 6z23C 6z24C 6qweS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 30823.643 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaKPC-4, blaKPC-2 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: B1PL86, UniProt: Q9F663*PLUS, beta-lactamase | ||||||||
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#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-CAZ / | #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.54 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 1.8 M ammonium sulphate, 5% ethanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.81001 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 12, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.81001 Å / Relative weight: 1 |
Reflection | Resolution: 1.24→55.74 Å / Num. obs: 73167 / % possible obs: 96.8 % / Redundancy: 13.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.038 / Rrim(I) all: 0.141 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.24→1.26 Å / Rmerge(I) obs: 2.827 / Mean I/σ(I) obs: 1 / Num. unique obs: 3483 / CC1/2: 0.747 / Rpim(I) all: 1.114 / Rrim(I) all: 3.04 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6QWE Resolution: 1.24→55.741 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 19.75
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 83.75 Å2 / Biso mean: 21.9467 Å2 / Biso min: 10 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.24→55.741 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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