+Open data
-Basic information
Entry | Database: PDB / ID: 6pbn | |||||||||||||||
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Title | Pseudopaline Dehydrogenase with (R)-Pseudopaline Soaked 1 hour | |||||||||||||||
Components | Pseudopaline Dehdyrogenase | |||||||||||||||
Keywords | BIOSYNTHETIC PROTEIN / Opine Metallophore Dehydrogenase Enzyme | |||||||||||||||
Function / homology | Function and homology information Oxidoreductases; Acting on the CH-NH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | Pseudomonas aeruginosa (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | |||||||||||||||
Authors | McFarlane, J.S. / Lamb, A.L. | |||||||||||||||
Funding support | United States, 4items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6pbn.cif.gz | 334.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pbn.ent.gz | 272.7 KB | Display | PDB format |
PDBx/mmJSON format | 6pbn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6pbn_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 6pbn_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 6pbn_validation.xml.gz | 38.7 KB | Display | |
Data in CIF | 6pbn_validation.cif.gz | 57.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pb/6pbn ftp://data.pdbj.org/pub/pdb/validation_reports/pb/6pbn | HTTPS FTP |
-Related structure data
Related structure data | 6pbmC 6pbpC 6pbtC 6c4nS S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#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 |
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-Non-polymers , 5 types, 635 molecules
#2: Chemical | #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-AKG / | #5: Chemical | ChemComp-O77 / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | 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: 2.35 Å3/Da / Density % sol: 47.72 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 260 mM ammonium formate, and 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 8, 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: 1.65→39.96 Å / Num. obs: 110062 / % possible obs: 98.5 % / Redundancy: 6.8 % / CC1/2: 0.998 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 1.65→1.68 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 4833 / CC1/2: 0.727 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6C4N Resolution: 1.65→39.96 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.77
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→39.96 Å
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Refine LS restraints |
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LS refinement shell |
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