[English] 日本語
Yorodumi- PDB-5top: Atomic Resolution X-Ray Crystal Structure of a Ruthenocene Conjug... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5top | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Atomic Resolution X-Ray Crystal Structure of a Ruthenocene Conjugated Beta-Lactam Antibiotic in Complex with CTX-M-14 S70G Beta-Lactamase | |||||||||
Components | Beta-lactamase | |||||||||
Keywords | HYDROLASE/ANTIBIOTIC / Beta-Lactamase / Organometallic / Ruthenocene / CTX-M-14 / HYDROLASE-ANTIBIOTIC complex | |||||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 Å | |||||||||
Authors | Lewandowski, E.M. / Chen, Y. | |||||||||
Funding support | United States, Poland, 2items
| |||||||||
Citation | Journal: FEBS J. / Year: 2018 Title: Mechanisms of proton relay and product release by Class A beta-lactamase at ultrahigh resolution. Authors: Lewandowski, E.M. / Lethbridge, K.G. / Sanishvili, R. / Skiba, J. / Kowalski, K. / Chen, Y. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5top.cif.gz | 258.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5top.ent.gz | 207.5 KB | Display | PDB format |
PDBx/mmJSON format | 5top.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5top_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5top_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 5top_validation.xml.gz | 28.1 KB | Display | |
Data in CIF | 5top_validation.cif.gz | 42.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/to/5top ftp://data.pdbj.org/pub/pdb/validation_reports/to/5top | HTTPS FTP |
-Related structure data
Related structure data | 5toyC 5vleC 4xxrS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 27953.488 Da / Num. of mol.: 2 / Mutation: S70G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CTX-M-14 / Production host: Escherichia coli (E. coli) / References: UniProt: H6UQI0, beta-lactamase |
---|
-Non-polymers , 6 types, 587 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-JSC / [( | #6: Chemical | ChemComp-7G4 / | #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.9 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.9 / Details: potassium phosphate |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Apr 1, 2015 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.18→50 Å / Num. obs: 133593 / % possible obs: 97.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 25.8 |
Reflection shell | Resolution: 1.18→1.2 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 4.3 / % possible all: 88.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4XXR Resolution: 1.18→50 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.976 / SU B: 0.942 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.035 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.345 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.18→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|