+Open data
-Basic information
Entry | Database: PDB / ID: 7d9f | |||||||||
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Title | SpdH Spermidine dehydrogenase SeMet 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 / SAD / Resolution: 1.85 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 | 7d9f.cif.gz | 333 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7d9f.ent.gz | 224.7 KB | Display | PDB format |
PDBx/mmJSON format | 7d9f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7d9f_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 7d9f_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 7d9f_validation.xml.gz | 54.9 KB | Display | |
Data in CIF | 7d9f_validation.cif.gz | 82.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d9/7d9f ftp://data.pdbj.org/pub/pdb/validation_reports/d9/7d9f | HTTPS FTP |
-Related 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 69702.172 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 |
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-Non-polymers , 5 types, 1218 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-SO4 / | #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: 2.12 Å3/Da / Density % sol: 41.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion 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: BL18U1 / Wavelength: 0.97778 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97778 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. obs: 95318 / % possible obs: 97.7 % / Redundancy: 6.4 % / Biso Wilson estimate: 18.27 Å2 / Rpim(I) all: 0.057 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 1.85→1.88 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4659 / Rpim(I) all: 0.345 / % possible all: 95.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.85→39.25 Å / SU ML: 0.1688 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.7431 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: 21.73 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→39.25 Å
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Refine LS restraints |
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LS refinement shell |
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