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Yorodumi- PDB-6w1g: Crystal structure of the hydroxyglutarate synthase from Pseudomon... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6w1g | ||||||
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Title | Crystal structure of the hydroxyglutarate synthase from Pseudomonas putida | ||||||
Components | Hydroxyglutarate synthase | ||||||
Keywords | LYASE / Decarboxylase Lysine catabolism | ||||||
Function / homology | Uncharacterised protein PF07063, DUF1338 / Domain of unknown function DUF1338 / 2-oxoadipate dioxygenase/decarboxylase / DUF1338 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Roll / Alpha Beta / NICKEL (II) ION / Metalloprotein, putative enzyme Function and homology information | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å | ||||||
Authors | Pereira, J.H. / Thompson, M.G. / Blake-Hedges, J.M. / Keasling, J.D. / Adams, P.D. | ||||||
Citation | Journal: Nat Commun / Year: 2020 Title: An iron (II) dependent oxygenase performs the last missing step of plant lysine catabolism. Authors: Thompson, M.G. / Blake-Hedges, J.M. / Pereira, J.H. / Hangasky, J.A. / Belcher, M.S. / Moore, W.M. / Barajas, J.F. / Cruz-Morales, P. / Washington, L.J. / Haushalter, R.W. / Eiben, C.B. / ...Authors: Thompson, M.G. / Blake-Hedges, J.M. / Pereira, J.H. / Hangasky, J.A. / Belcher, M.S. / Moore, W.M. / Barajas, J.F. / Cruz-Morales, P. / Washington, L.J. / Haushalter, R.W. / Eiben, C.B. / Liu, Y. / Skyrud, W. / Benites, V.T. / Barnum, T.P. / Baidoo, E.E.K. / Scheller, H.V. / Marletta, M.A. / Shih, P.M. / Adams, P.D. / Keasling, J.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6w1g.cif.gz | 300 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6w1g.ent.gz | 237.2 KB | Display | PDB format |
PDBx/mmJSON format | 6w1g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w1/6w1g ftp://data.pdbj.org/pub/pdb/validation_reports/w1/6w1g | HTTPS FTP |
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-Related structure data
Related structure data | 6w1hC 6w1kC 2rjbS 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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Unit cell |
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-Components
#1: Protein | Mass: 51427.805 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: ydcJ, PP_5260 / Production host: Escherichia coli (E. coli) / References: UniProt: Q88CC1 |
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#2: Chemical | ChemComp-NI / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.53 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Ammonium Fluoride, 20 % PEG 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 16, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.14→52.38 Å / Num. obs: 164046 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 13 Å2 / CC1/2: 0.999 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 1.14→1.18 Å / Num. unique obs: 16167 / CC1/2: 0.666 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2RJB Resolution: 1.14→52.38 Å / SU ML: 0.1029 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 14.7214
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.97 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.14→52.38 Å
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Refine LS restraints |
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LS refinement shell |
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