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Yorodumi- PDB-6cf3: Ethylene forming enzyme Y306A variant in complex with manganese a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6cf3 | ||||||
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Title | Ethylene forming enzyme Y306A variant in complex with manganese and 2-oxoglutarate | ||||||
Components | 2-oxoglutarate-dependent ethylene/succinate-forming enzyme | ||||||
Keywords | OXIDOREDUCTASE / manganese / 2-oxoglutarate / L-arginine / split occupancy / partially occupied / tyrosine to alanine / ethylene glycol / variant induced fold changes | ||||||
Function / homology | Function and homology information 2-oxoglutarate dioxygenase (ethene-forming) / 2-oxoglutarate/L-arginine monooxygenase/decarboxylase (succinate-forming) / 2-oxoglutarate oxygenase/decarboxylase (ethylene-forming) activity / ethylene biosynthetic process / dioxygenase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas savastanoi pv. phaseolicola (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.12 Å | ||||||
Authors | Fellner, M. / Martinez, S. / Hu, J. / Hausinger, R.P. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2024 Title: Structural, Spectroscopic, and Computational Insights from Canavanine-Bound and Two Catalytically Compromised Variants of the Ethylene-Forming Enzyme. Authors: Chatterjee, S. / Fellner, M. / Rankin, J. / Thomas, M.G. / J S Rifayee, S.B. / Christov, C.Z. / Hu, J. / Hausinger, R.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6cf3.cif.gz | 213.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cf3.ent.gz | 171.3 KB | Display | PDB format |
PDBx/mmJSON format | 6cf3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cf/6cf3 ftp://data.pdbj.org/pub/pdb/validation_reports/cf/6cf3 | HTTPS FTP |
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-Related structure data
Related structure data | 6cbaC 8uc2C 5v2yS 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: 39624.668 Da / Num. of mol.: 1 / Mutation: N-terminal fusion to SH, Y306A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas savastanoi pv. phaseolicola (bacteria) Gene: efe / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 Gold (DE3) References: UniProt: P32021, 2-oxoglutarate dioxygenase (ethene-forming), EC: 1.14.11.34 |
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#2: Chemical | ChemComp-MN / |
#3: Chemical | ChemComp-AKG / |
#4: Chemical | ChemComp-EDO / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.98 % / Mosaicity: 0.2 ° |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.5 ul 64 mg/ml EFE-Y306A (1 mM manganese chloride, 25 mM HEPES pH 8.0, 1 mM TCEP, 3 mM L-Arginine, 3 mM 2-oxoglutarate) was mixed with 0.5 ul reservoir solution. The sitting drop reservoir ...Details: 0.5 ul 64 mg/ml EFE-Y306A (1 mM manganese chloride, 25 mM HEPES pH 8.0, 1 mM TCEP, 3 mM L-Arginine, 3 mM 2-oxoglutarate) was mixed with 0.5 ul reservoir solution. The sitting drop reservoir of 200 ul contained 25% w/v Polyethylene glycol 3,350, 0.1 M Bis-Tris pH 6.5, 0.2 M sodium chloride. The crystal was soaked for five minutes in 25% w/v Ethylene glycol, 75% reservoir solution before freezing it. |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9762 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 3, 2017 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.12→44.37 Å / Num. obs: 125336 / % possible obs: 98.2 % / Redundancy: 5.9 % / Biso Wilson estimate: 8.62 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.053 / Rrim(I) all: 0.133 / Net I/σ(I): 7.9 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5V2Y Resolution: 1.12→44.37 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 14.97
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 49.16 Å2 / Biso mean: 14.2202 Å2 / Biso min: 4.9 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.12→44.37 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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