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Yorodumi- PDB-6w1k: Crystal structure of the hydroxyglutarate synthase in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6w1k | ||||||
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Title | Crystal structure of the hydroxyglutarate synthase in complex with 2-oxoadipate from Oryza sativa | ||||||
Components | Hydroxyglutarate synthase | ||||||
Keywords | LYASE / Decarboxylase Lysine catabolism | ||||||
Function / homology | Domain of unknown function DUF1338 / 2-oxoadipate dioxygenase/decarboxylase / DUF1338 / NICKEL (II) ION / 2-OXOADIPIC ACID / Os10g0463800 protein / DUF1338 domain-containing protein Function and homology information | ||||||
Biological species | Oryza sativa (Asian cultivated rice) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 | 6w1k.cif.gz | 763.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6w1k.ent.gz | 620 KB | Display | PDB format |
PDBx/mmJSON format | 6w1k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6w1k_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 6w1k_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6w1k_validation.xml.gz | 56.9 KB | Display | |
Data in CIF | 6w1k_validation.cif.gz | 84 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w1/6w1k ftp://data.pdbj.org/pub/pdb/validation_reports/w1/6w1k | HTTPS FTP |
-Related structure data
Related structure data | 6w1gC 6w1hC 3lhoS 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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Unit cell |
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-Components
#1: Protein | Mass: 36140.234 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa (Asian cultivated rice) / Gene: OsJ_31810, OSJNBa0071K18.7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8H916, UniProt: Q337M4*PLUS #2: Chemical | ChemComp-NI / #3: Chemical | ChemComp-OOG / #4: Chemical | ChemComp-SO4 / #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: 3.19 Å3/Da / Density % sol: 61.5 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.01 M Magnesium Chloride, 0.05 M MES pH 5.6, 1.8 M Lithium Sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 19, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→39.8 Å / Num. obs: 156493 / % possible obs: 98.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 29.19 Å2 / CC1/2: 0.998 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 1.85→1.91 Å / Num. unique obs: 15364 / CC1/2: 0.517 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LHO Resolution: 1.85→39.79 Å / SU ML: 0.189 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.4898
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.28 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→39.79 Å
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Refine LS restraints |
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LS refinement shell |
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