[English] 日本語
Yorodumi- PDB-6r79: Structure of IMP-13 metallo-beta-lactamase in apo form (loop open) -
+Open data
-Basic information
Entry | Database: PDB / ID: 6r79 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of IMP-13 metallo-beta-lactamase in apo form (loop open) | ||||||||||||
Components | Beta-lactamase | ||||||||||||
Keywords | HYDROLASE / metallo-beta-lactamase beta-lactamase | ||||||||||||
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 | Pseudomonas aeruginosa (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å | ||||||||||||
Authors | Zak, K.M. / Softley, C. / Kolonko, M. / Sattler, M. / Popowicz, G.M. | ||||||||||||
Funding support | Germany, Poland, 3items
| ||||||||||||
Citation | Journal: Antimicrob.Agents Chemother. / Year: 2020 Title: Structure and Molecular Recognition Mechanism of IMP-13 Metallo-beta-Lactamase. Authors: Softley, C.A. / Zak, K.M. / Bostock, M.J. / Fino, R. / Zhou, R.X. / Kolonko, M. / Mejdi-Nitiu, R. / Meyer, H. / Sattler, M. / Popowicz, G.M. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6r79.cif.gz | 208 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6r79.ent.gz | 160.7 KB | Display | PDB format |
PDBx/mmJSON format | 6r79.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r7/6r79 ftp://data.pdbj.org/pub/pdb/validation_reports/r7/6r79 | HTTPS FTP |
---|
-Related structure data
Related structure data | 6r73C 6r78SC 6rzrC 6rzsC 6s0hC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
4 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / Refine code: 0
NCS ensembles :
|
-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 24567.004 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: bla-imp13, bla-IMP13, blaIMP-13 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7WYA8, beta-lactamase |
---|
-Non-polymers , 7 types, 930 molecules
#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-BME / #4: Chemical | ChemComp-GLY / #5: Chemical | ChemComp-ZN / #6: Chemical | ChemComp-NA / | #7: Chemical | ChemComp-PO4 / | #8: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
---|
-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.3 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris pH 8.5, 25% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 193 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.966 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 5, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→61.55 Å / Num. obs: 67023 / % possible obs: 94.65 % / Redundancy: 1.7 % / CC1/2: 0.997 / Net I/σ(I): 9.58 |
Reflection shell | Resolution: 1.9→1.968 Å / Num. unique obs: 6850 |
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6R78 Resolution: 1.9→61.55 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.608 / SU ML: 0.126 / SU R Cruickshank DPI: 0.1638 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.164 / ESU R Free: 0.145
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 141.68 Å2 / Biso mean: 29.658 Å2 / Biso min: 12.35 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→61.55 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|