+Open data
-Basic information
Entry | Database: PDB / ID: 8af7 | ||||||
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Title | Room temperature SSX crystal structure of CTX-M-14 (10K dataset) | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / beta-lactamase / serial crystallography / SSX / TapeDrive | ||||||
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: 1.55 Å | ||||||
Authors | Oberthuer, D. / Perbandt, M. / Prester, A. / Rohde, H. / Betzel, C. / Yefanov, O. | ||||||
Funding support | 1items
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Citation | Journal: Iucrj / Year: 2022 Title: Rapid and efficient room-temperature serial synchrotron crystallography using the CFEL TapeDrive. Authors: Zielinski, K.A. / Prester, A. / Andaleeb, H. / Bui, S. / Yefanov, O. / Catapano, L. / Henkel, A. / Wiedorn, M.O. / Lorbeer, O. / Crosas, E. / Meyer, J. / Mariani, V. / Domaracky, M. / White, ...Authors: Zielinski, K.A. / Prester, A. / Andaleeb, H. / Bui, S. / Yefanov, O. / Catapano, L. / Henkel, A. / Wiedorn, M.O. / Lorbeer, O. / Crosas, E. / Meyer, J. / Mariani, V. / Domaracky, M. / White, T.A. / Fleckenstein, H. / Sarrou, I. / Werner, N. / Betzel, C. / Rohde, H. / Aepfelbacher, M. / Chapman, H.N. / Perbandt, M. / Steiner, R.A. / Oberthuer, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8af7.cif.gz | 192.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8af7.ent.gz | 133.9 KB | Display | PDB format |
PDBx/mmJSON format | 8af7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/af/8af7 ftp://data.pdbj.org/pub/pdb/validation_reports/af/8af7 | HTTPS FTP |
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-Related structure data
Related structure data | 7qarC 7zpvC 7zq0C 8af4C 8af5C 8af6C 8af8C 6gthS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 27771.314 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: ctx-m-14 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D2D9A0, beta-lactamase |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.19 % |
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Crystal grow | Temperature: 293 K / Method: batch mode / pH: 4.5 Details: CTX-M-14 was produced, purified and crystallized as before, with a slight modification in crystallization conditions to obtain slightly bigger crystals which roughly match the X-ray focal ...Details: CTX-M-14 was produced, purified and crystallized as before, with a slight modification in crystallization conditions to obtain slightly bigger crystals which roughly match the X-ray focal spot. For this purpose, a 50% CTX-M-14 solution (22 mg/ml) was mixed with a 45% precipitant solution (40% PEG8000, 200 mM lithium sulfate, 100 mM sodium acetate, pH 4.5) and with a 5% undiluted seed stock in batch crystallization setups, resulting in crystals with a homogeneous size distribution of 11-15 um after 90 minutes. The crystals were centrifuged at 200xg for 5 min and the supernatant was replaced with a stabilization buffer (28% PEG8000, 140 mM lithium sulfate, 70 mM sodium acetate, pH 4.5) to stop further crystal growth. |
-Data collection
Diffraction | Mean temperature: 295 K / Serial crystal experiment: Y |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→17.77 Å / Num. obs: 36504 / % possible obs: 99.98 % / Redundancy: 114 % / Biso Wilson estimate: 23.58 Å2 / CC1/2: 0.815 / CC star: 0.948 / R split: 0.278 / Net I/σ(I): 3.25 |
Reflection shell | Resolution: 1.55→1.58 Å / Redundancy: 65 % / Mean I/σ(I) obs: 0.62 / Num. unique obs: 3514 / CC1/2: 0.268 / CC star: 0.65 / R split: 1.72 / % possible all: 100 |
Serial crystallography sample delivery | Description: TapeDrive / Method: injection |
Serial crystallography sample delivery injection | Description: TapeDrive / Flow rate: 2 µL/min / Injector diameter: 180 µm |
Serial crystallography data reduction | Frames total: 10382 / Lattices indexed: 4286 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6GTH Resolution: 1.55→16.54 Å / SU ML: 0.2159 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.9629 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 32.61 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→16.54 Å
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Refine LS restraints |
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LS refinement shell |
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