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Yorodumi- PDB-7jso: P. syringae AldA Indole-3-Acetaldehyde Dehydrogenase C302A mutant... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7jso | |||||||||||||||
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Title | P. syringae AldA Indole-3-Acetaldehyde Dehydrogenase C302A mutant in complex with NAD+ and IAA | |||||||||||||||
Components | Aldehyde dehydrogenase family protein | |||||||||||||||
Keywords | OXIDOREDUCTASE / aldehyde dehydrogenase / auxin | |||||||||||||||
Function / homology | Function and homology information | |||||||||||||||
Biological species | Pseudomonas syringae pv. tomato (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.848 Å | |||||||||||||||
Authors | Jez, J.M. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Biosci.Rep. / Year: 2020 Title: Investigating the reaction and substrate preference of indole-3-acetaldehyde dehydrogenase from the plant pathogen Pseudomonas syringae PtoDC3000. Authors: Zhang, K. / Lee, J.S. / Liu, R. / Chan, Z.T. / Dawson, T.J. / De Togni, E.S. / Edwards, C.T. / Eng, I.K. / Gao, A.R. / Goicouria, L.A. / Hall, E.M. / Hu, K.A. / Huang, K. / Kizhner, A. / ...Authors: Zhang, K. / Lee, J.S. / Liu, R. / Chan, Z.T. / Dawson, T.J. / De Togni, E.S. / Edwards, C.T. / Eng, I.K. / Gao, A.R. / Goicouria, L.A. / Hall, E.M. / Hu, K.A. / Huang, K. / Kizhner, A. / Kodama, K.C. / Lin, A.Z. / Liu, J.Y. / Lu, A.Y. / Peng, O.W. / Ryu, E.P. / Shi, S. / Sorkin, M.L. / Walker, P.L. / Wang, G.J. / Xu, M.C. / Yang, R.S. / Cascella, B. / Cruz, W. / Holland, C.K. / McClerkin, S.A. / Kunkel, B.N. / Lee, S.G. / Jez, J.M. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7jso.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7jso.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 7jso.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/js/7jso ftp://data.pdbj.org/pub/pdb/validation_reports/js/7jso | HTTPS FTP |
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-Related structure data
Related structure data | 5iuwS S: Starting model for refinement |
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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: 52747.762 Da / Num. of mol.: 8 / Mutation: C302A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas syringae pv. tomato (strain ATCC BAA-871 / DC3000) (bacteria) Strain: ATCC BAA-871 / DC3000 / Gene: PSPTO_0092 / Production host: Escherichia coli (E. coli) / References: UniProt: Q88BC5 #2: Chemical | ChemComp-NAI / #3: Chemical | ChemComp-IAC / Has ligand of interest | N | |
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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: 2.71 Å3/Da / Density % sol: 54.58 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 24% PEG-1000, 100 mM Tris-HCl (pH 7.0), 2 mM IAA, and 5 mM NAD+ |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 4, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.848→47.9 Å / Num. obs: 103830 / % possible obs: 98.3 % / Redundancy: 5.4 % / Biso Wilson estimate: 22.23 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 2.848→2.92 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 5.4 / Num. unique obs: 5374 / Rsym value: 0.241 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5IUW Resolution: 2.848→47.888 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 38.41 / Stereochemistry target values: ML
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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 max: 119.14 Å2 / Biso mean: 36.3547 Å2 / Biso min: 1.65 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.848→47.888 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 381.0329 Å / Origin y: 81.9742 Å / Origin z: 58.9785 Å
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Refinement TLS group |
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