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Yorodumi- PDB-5vka: Ethylene forming enzyme in complex with manganese, 2-oxoglutarate... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vka | ||||||
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Title | Ethylene forming enzyme in complex with manganese, 2-oxoglutarate and N-omega-hydroxy-L-arginine | ||||||
Components | 2-oxoglutarate-dependent ethylene/succinate-forming enzyme | ||||||
Keywords | OXIDOREDUCTASE / 2-oxoglutarate / N-omega-hydroxy-L-arginine | ||||||
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: 1.169 Å | ||||||
Authors | Fellner, M. / Martinez, S. / Hu, J. / Hausinger, R.P. | ||||||
Citation | Journal: J. Am. Chem. Soc. / Year: 2017 Title: Structures and Mechanisms of the Non-Heme Fe(II)- and 2-Oxoglutarate-Dependent Ethylene-Forming Enzyme: Substrate Binding Creates a Twist. Authors: Martinez, S. / Fellner, M. / Herr, C.Q. / Ritchie, A. / 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 | 5vka.cif.gz | 161.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vka.ent.gz | 125.5 KB | Display | PDB format |
PDBx/mmJSON format | 5vka.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vk/5vka ftp://data.pdbj.org/pub/pdb/validation_reports/vk/5vka | HTTPS FTP |
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-Related structure data
Related structure data | 5v2tC 5v2uC 5v2vC 5v2xC 5v2yC 5v2zSC 5v31C 5v32C 5v34C 5vkbC C: citing same article (ref.) 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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Unit cell |
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-Components
#1: Protein | Mass: 40138.809 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas savastanoi pv. phaseolicola (bacteria) Gene: efe / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / 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-HAR / |
#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: 2.2 Å3/Da / Density % sol: 44.18 % / Mosaicity: 0.05 ° |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.5 ul 72 mg/ml selenomethionine containing EFE (9 mM manganese chloride, 25 mM HEPES pH 8.0, 1 mM TCEP) was mixed with 0.5 ul reservoir solution of 10 mM N-omega-hydroxy-L-arginine, and 0.2 ...Details: 0.5 ul 72 mg/ml selenomethionine containing EFE (9 mM manganese chloride, 25 mM HEPES pH 8.0, 1 mM TCEP) was mixed with 0.5 ul reservoir solution of 10 mM N-omega-hydroxy-L-arginine, and 0.2 uL of 100 mM 2OG. The sitting drop reservoir of 200 ul contained 20% w/v Polyethylene glycol 6,000, 0.1 M Tris pH 8.0, 0.2 M Lithium chloride. The crystal was soaked for about a minute 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-F / Wavelength: 0.9787 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 16, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 1.169→48.58 Å / Num. obs: 118142 / % possible obs: 99.2 % / Redundancy: 5.7 % / Biso Wilson estimate: 9.78 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.042 / Rrim(I) all: 0.103 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 1.169→1.19 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.593 / Num. unique obs: 5146 / CC1/2: 0.752 / Rpim(I) all: 0.339 / Rrim(I) all: 0.687 / % possible all: 87.9 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5V2Z Resolution: 1.169→38.701 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.9 / Phase error: 19.7
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 76.49 Å2 / Biso mean: 16.2119 Å2 / Biso min: 4.02 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.169→38.701 Å
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Refine LS restraints |
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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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