+Open data
-Basic information
Entry | Database: PDB / ID: 6pbt | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Pseudopaline Dehydrogenase with (R)-Pseudopaline Soaked 2 hours | |||||||||||||||
Components | Pseudopaline Dehydrogenase | |||||||||||||||
Keywords | BIOSYNTHETIC PROTEIN / Opine Metallophore Dehydrogenase Enzyme | |||||||||||||||
Function / homology | Oxidoreductases; Acting on the CH-NH group of donors; With NAD+ or NADP+ as acceptor / Opine metallophore dehydrogenase / Staphylopine dehydrogenase / oxidoreductase activity / NAD(P)-binding domain superfamily / plasma membrane / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / N-[(3S)-3-amino-3-carboxypropyl]-L-histidine / Pseudopaline synthase Function and homology information | |||||||||||||||
Biological species | Pseudomonas aeruginosa (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å | |||||||||||||||
Authors | McFarlane, J.S. / Lamb, A.L. | |||||||||||||||
Funding support | United States, 4items
| |||||||||||||||
Citation | Journal: J.Biol.Chem. / Year: 2019 Title: Staphylopine and pseudopaline dehydrogenase from bacterial pathogens catalyze reversible reactions and produce stereospecific metallophores. Authors: McFarlane, J.S. / Zhang, J. / Wang, S. / Lei, X. / Moran, G.R. / Lamb, A.L. | |||||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6pbt.cif.gz | 320.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6pbt.ent.gz | 264.2 KB | Display | PDB format |
PDBx/mmJSON format | 6pbt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6pbt_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6pbt_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6pbt_validation.xml.gz | 33.1 KB | Display | |
Data in CIF | 6pbt_validation.cif.gz | 47.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pb/6pbt ftp://data.pdbj.org/pub/pdb/validation_reports/pb/6pbt | HTTPS FTP |
-Related structure data
Related structure data | 6pbmC 6pbnC 6pbpC 6c4nS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 49578.500 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: PA4835 / Production host: Escherichia coli (E. coli) References: UniProt: Q9HUX5, Oxidoreductases; Acting on the CH-NH group of donors; With NAD+ or NADP+ as acceptor #2: Chemical | #3: Chemical | ChemComp-O77 / | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.98 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 270 mM ammonium formate, and 28% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 11, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.18→39.78 Å / Num. obs: 48010 / % possible obs: 97.8 % / Redundancy: 6.8 % / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2.18→2.24 Å / Num. unique obs: 3584 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6C4N Resolution: 2.18→39.78 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.42
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.18→39.78 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|