+Open data
-Basic information
Entry | Database: PDB / ID: 7d9h | |||||||||
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Title | SpdH Spermidine dehydrogenase N33 truncation structure | |||||||||
Components | Spermidine dehydrogenase, SpdH | |||||||||
Keywords | OXIDOREDUCTASE / SpdH / Spermidine dehydrogenase / Heme-containing monoamine oxidase / Pseudomonas aeruginosa PAO1. | |||||||||
Function / homology | Function and homology information phytoene dehydrogenase activity / carotenoid biosynthetic process / oxidoreductase activity / nucleotide binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Pseudomonas aeruginosa (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å | |||||||||
Authors | Che, S. / Zhang, Q. / Bartlam, M. | |||||||||
Funding support | China, 2items
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Citation | Journal: Febs J. / Year: 2022 Title: Structure of Pseudomonas aeruginosa spermidine dehydrogenase: a polyamine oxidase with a novel heme-binding fold. Authors: Che, S. / Liang, Y. / Chen, Y. / Wu, W. / Liu, R. / Zhang, Q. / Bartlam, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7d9h.cif.gz | 320.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7d9h.ent.gz | 204.4 KB | Display | PDB format |
PDBx/mmJSON format | 7d9h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7d9h_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 7d9h_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 7d9h_validation.xml.gz | 49.8 KB | Display | |
Data in CIF | 7d9h_validation.cif.gz | 72.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d9/7d9h ftp://data.pdbj.org/pub/pdb/validation_reports/d9/7d9h | HTTPS FTP |
-Related structure data
Related structure data | 7d9fSC 7d9gC 7d9iC 7d9jC 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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Unit cell |
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-Components
#1: Protein | Mass: 65555.867 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) Gene: spdH, PA3713 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HXS8, EC: 1.5.99.6 #2: Chemical | #3: Chemical | #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: 2.24 Å3/Da / Density % sol: 45.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.5 Details: 0.1M Bis Tris pH6.5, 20% w/v polyethylene glycol (PEG) 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.977 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 14, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 48990 / % possible obs: 96.8 % / Redundancy: 3 % / Biso Wilson estimate: 28.43 Å2 / Rpim(I) all: 0.037 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 3 % / Mean I/σ(I) obs: 7.7 / Num. unique obs: 2445 / Rpim(I) all: 0.089 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7D9F Resolution: 2.31→38.74 Å / SU ML: 0.2546 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.7333 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.47 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.31→38.74 Å
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Refine LS restraints |
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LS refinement shell |
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