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Yorodumi- PDB-6eum: CRYSTAL STRUCTURE OF BCII METALLO-BETA-LACTAMASE IN COMPLEX WITH ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6eum | |||||||||
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Title | CRYSTAL STRUCTURE OF BCII METALLO-BETA-LACTAMASE IN COMPLEX WITH DZ-307 | |||||||||
Components | Metallo-beta-lactamase type 2 | |||||||||
Keywords | HYDROLASE / ANTIMICROBIAL RESISTANCE / METALLO BETA LACTAMASE / INHIBITOR | |||||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding Similarity search - Function | |||||||||
Biological species | Bacillus cereus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 Å | |||||||||
Authors | Stepanovs, D. / McDonough, M.A. / Schofield, C.J. / Zhang, D. / El-Husseiny, A. / Brem, J. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Bioorg. Med. Chem. / Year: 2018 Title: Structure activity relationship studies on rhodanines and derived enethiol inhibitors of metallo-beta-lactamases. Authors: Zhang, D. / Markoulides, M.S. / Stepanovs, D. / Rydzik, A.M. / El-Hussein, A. / Bon, C. / Kamps, J.J.A.G. / Umland, K.D. / Collins, P.M. / Cahill, S.T. / Wang, D.Y. / von Delft, F. / Brem, J. ...Authors: Zhang, D. / Markoulides, M.S. / Stepanovs, D. / Rydzik, A.M. / El-Hussein, A. / Bon, C. / Kamps, J.J.A.G. / Umland, K.D. / Collins, P.M. / Cahill, S.T. / Wang, D.Y. / von Delft, F. / Brem, J. / McDonough, M.A. / Schofield, C.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6eum.cif.gz | 120.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6eum.ent.gz | 92.1 KB | Display | PDB format |
PDBx/mmJSON format | 6eum.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6eum_validation.pdf.gz | 789.5 KB | Display | wwPDB validaton report |
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Full document | 6eum_full_validation.pdf.gz | 791 KB | Display | |
Data in XML | 6eum_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | 6eum_validation.cif.gz | 20.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eu/6eum ftp://data.pdbj.org/pub/pdb/validation_reports/eu/6eum | HTTPS FTP |
-Related structure data
Related structure data | 5jmxC 6ew3C 6eweC 6f2nC 4tytS C: citing same article (ref.) 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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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 25011.533 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: blm / Plasmid: PET9a / Production host: Escherichia coli (E. coli) / References: UniProt: P04190, beta-lactamase |
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-Non-polymers , 5 types, 246 molecules
#2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Chemical | ChemComp-BY5 / (~{ | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has protein modification | 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: 2.3 Å3/Da / Density % sol: 45 % / Description: rhombohedron |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 1MM TCEP, 5MM DZ-307, 50MM HEPES pH7.5, 100MM NACL, 0.1MM ZNCL2, 0.1M MAGNESIUM FORMATE, 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.95 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 11, 2016 |
Radiation | Monochromator: double Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 1.18→35.5 Å / Num. obs: 72015 / % possible obs: 97.5 % / Redundancy: 16.5 % / Biso Wilson estimate: 12.306 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.025 / Rrim(I) all: 0.101 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 1.18→1.21 Å / Redundancy: 17 % / Rmerge(I) obs: 2.489 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 5168 / CC1/2: 0.563 / Rpim(I) all: 0.631 / Rrim(I) all: 2.642 / % possible all: 94.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4TYT Resolution: 1.18→19.529 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 15.96
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||
Displacement parameters | Biso max: 88.68 Å2 / Biso mean: 24.4404 Å2 / Biso min: 10.8 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.18→19.529 Å
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LS refinement shell | Resolution: 1.18→1.1969 Å
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