+Open data
-Basic information
Entry | Database: PDB / ID: 6pop | ||||||
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Title | Crystal structure of DauA in complex with NADP+ | ||||||
Components | Aldehyde dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Dehydrogenase | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor Similarity search - Function | ||||||
Biological species | Pseudoalteromonas fuliginea (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.147 Å | ||||||
Authors | Pluvinage, B. / Boraston, A.B. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Commun Biol / Year: 2019 Title: Insights into the kappa / iota-carrageenan metabolism pathway of some marinePseudoalteromonasspecies. Authors: Hettle, A.G. / Hobbs, J.K. / Pluvinage, B. / Vickers, C. / Abe, K.T. / Salama-Alber, O. / McGuire, B.E. / Hehemann, J.H. / Hui, J.P.M. / Berrue, F. / Banskota, A. / Zhang, J. / Bottos, E.M. ...Authors: Hettle, A.G. / Hobbs, J.K. / Pluvinage, B. / Vickers, C. / Abe, K.T. / Salama-Alber, O. / McGuire, B.E. / Hehemann, J.H. / Hui, J.P.M. / Berrue, F. / Banskota, A. / Zhang, J. / Bottos, E.M. / Van Hamme, J. / Boraston, A.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6pop.cif.gz | 544.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pop.ent.gz | 445.5 KB | Display | PDB format |
PDBx/mmJSON format | 6pop.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/po/6pop ftp://data.pdbj.org/pub/pdb/validation_reports/po/6pop | HTTPS FTP |
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-Related structure data
Related structure data | 6pnuSC 6prmC 6psmC 6psoC 6pt4C 6pt6C 6pt9C 6ptkC 6ptmC 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 53377.258 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudoalteromonas fuliginea (bacteria) / Gene: DC53_13140 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A063KJS9*PLUS #2: Chemical | ChemComp-NAP / #3: Chemical | ChemComp-EDO / #4: Chemical | #5: Water | ChemComp-HOH / | 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: 2.46 Å3/Da / Density % sol: 49.92 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.2 M sodium acetate trihydrate, 0.1 M Bis-Tris and 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Jul 14, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.147→39.853 Å / Num. obs: 167353 / % possible obs: 99.2 % / Redundancy: 5.4 % / CC1/2: 0.989 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.072 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.15→2.18 Å / Rmerge(I) obs: 0.579 / Num. unique obs: 8002 / CC1/2: 0.671 / Rpim(I) all: 0.328 / % possible all: 98.1 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6PNU Resolution: 2.147→39.853 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.37
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77.46 Å2 / Biso mean: 36.1514 Å2 / Biso min: 17.57 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.147→39.853 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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