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Yorodumi- PDB-6td9: X-ray structure of mature PA1624 from Pseudomonas aeruginosa PAO1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6td9 | ||||||
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Title | X-ray structure of mature PA1624 from Pseudomonas aeruginosa PAO1 | ||||||
Components | PA1624 | ||||||
Keywords | UNKNOWN FUNCTION / periplasmic protein / unique fold | ||||||
Function / homology | Protein of unknown function DUF4892 / Domain of unknown function (DUF4892) / periplasmic space / PHOSPHATE ION / Uncharacterized protein PA1624 Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa PAO1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.96 Å | ||||||
Authors | Feiler, C.G. / Blankenfeldt, W. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2020 Title: The hypothetical periplasmic protein PA1624 from Pseudomonas aeruginosa folds into a unique two-domain structure. Authors: Feiler, C.G. / Weiss, M.S. / Blankenfeldt, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6td9.cif.gz | 237.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6td9.ent.gz | 161.5 KB | Display | PDB format |
PDBx/mmJSON format | 6td9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/td/6td9 ftp://data.pdbj.org/pub/pdb/validation_reports/td/6td9 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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: 27750.184 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: PA1624 / Plasmid: p10$ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9I398 #2: Chemical | ChemComp-EDO / | #3: Chemical | ChemComp-EPE / | #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: 2.29 Å3/Da / Density % sol: 46.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.1 / Details: 0.15 M NaAc, 0.1 M HEPES, 23.3% PEG 4000 / PH range: 7.0-8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.979531 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 25, 2014 |
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979531 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→48 Å / Num. obs: 36764 / % possible obs: 99.41 % / Redundancy: 91 % / Biso Wilson estimate: 21.48 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.2238 / Rpim(I) all: 0.02321 / Rrim(I) all: 0.225 / Net I/σ(I): 27.08 |
Reflection shell | Resolution: 1.96→2.03 Å / Redundancy: 36.4 % / Rmerge(I) obs: 1.739 / Mean I/σ(I) obs: 2.58 / Num. unique obs: 3576 / CC1/2: 0.746 / Rpim(I) all: 0.2816 / Rrim(I) all: 1.763 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.96→47.49 Å / SU ML: 0.2394 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.5329
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.77 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.96→47.49 Å
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Refine LS restraints |
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LS refinement shell |
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