+Open data
-Basic information
Entry | Database: PDB / ID: 6jkw | ||||||
---|---|---|---|---|---|---|---|
Title | Seleno-methionine PNGM-1 from deep-sea sediment metagenome | ||||||
Components | Metallo-beta-lactamases PNGM-1 | ||||||
Keywords | TRANSFERASE / MBLs / Zinc binding motif / antibiotic resistance / metagenome / Structural Genomics / PSI-Biology | ||||||
Biological species | Acinetobacter baumannii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.29 Å | ||||||
Authors | Hong, M.K. / Park, K.S. / Jeon, J.H. / Lee, J.H. / Park, Y.S. / Lee, S.H. / Kang, L.W. | ||||||
Citation | Journal: Journal of Global Antimicrobial Resistance / Year: 2018 Title: PNGM 1 a novel subclass B3 metallo beta lactamase from a deep sea sediment metagenome Authors: Kang, L.W. / Lee, S.H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6jkw.cif.gz | 579.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6jkw.ent.gz | 500.2 KB | Display | PDB format |
PDBx/mmJSON format | 6jkw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jk/6jkw ftp://data.pdbj.org/pub/pdb/validation_reports/jk/6jkw | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 42498.727 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) #2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 45.97 % |
---|---|
Crystal grow | Temperature: 287 K / Method: evaporation / pH: 7 / Details: 0.1M Tris-HCl, 0.2M MgCl2 and 10% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 8, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→34.93 Å / Num. obs: 137843 / % possible obs: 98.1 % / Redundancy: 3.8 % / Net I/σ(I): 4.7 |
Reflection shell | Resolution: 2.3→2.34 Å |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 2.29→34.93 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.925 / SU B: 7.994 / SU ML: 0.196 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.423 / ESU R Free: 0.278 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 128.57 Å2 / Biso mean: 32.866 Å2 / Biso min: 7.88 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.29→34.93 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.285→2.344 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|