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Open data
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Basic information
Entry | Database: PDB / ID: 5v2t | ||||||
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Title | Ethylene forming enzyme in complex with manganese and tartrate | ||||||
![]() | 2-oxoglutarate-dependent ethylene/succinate-forming enzyme | ||||||
![]() | OXIDOREDUCTASE / ethylene biosynthesis | ||||||
Function / homology | ![]() 2-oxoglutarate dioxygenase (ethene-forming) / 2-oxoglutarate/L-arginine monooxygenase/decarboxylase (succinate-forming) / 2-oxoglutarate oxygenase/decarboxylase (ethylene-forming) activity / ethylene biosynthetic process / 2-oxoglutarate-dependent dioxygenase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() ![]() | ||||||
![]() | Fellner, M. / Martinez, S. / Hu, J. / Hausinger, R.P. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 215.7 KB | Display | ![]() |
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PDB format | ![]() | 184 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.3 KB | Display | ![]() |
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Full document | ![]() | 441.5 KB | Display | |
Data in XML | ![]() | 18.8 KB | Display | |
Data in CIF | ![]() | 29.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5v2uC ![]() 5v2vC ![]() 5v2xC ![]() 5v2yC ![]() 5v2zC ![]() 5v31C ![]() 5v32C ![]() 5v34C ![]() 5vkaC ![]() 5vkbC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() Gene: efe / Plasmid: pET28 / Production host: ![]() ![]() References: UniProt: P32021, 2-oxoglutarate dioxygenase (ethene-forming), EC: 1.14.11.34 |
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#2: Chemical | ChemComp-MN / |
#3: Chemical | ChemComp-TLA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.91 % / Mosaicity: 0.12 ° |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 1 ul 59 mg/ml EFE (1.2 mM manganese chloride, 25 mM HEPES pH 8.0, 1 mM TCEP, + 0.720 mM 2-oxoglutarate, + 0.720 mM L-arginine) was mixed with 1 ul reservoir solution. The sitting drop ...Details: 1 ul 59 mg/ml EFE (1.2 mM manganese chloride, 25 mM HEPES pH 8.0, 1 mM TCEP, + 0.720 mM 2-oxoglutarate, + 0.720 mM L-arginine) was mixed with 1 ul reservoir solution. The sitting drop reservoir of 200 ul contained 1000 mM Potassium sodium tartrate, 100 mM MES/ Sodium hydroxide pH 6.0. The crystal was soaked for about a minute in 25% glycerol, 75% reservoir solution before freezing it. |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 25, 2016 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.227→48.991 Å / Num. obs: 222554 / % possible obs: 99.7 % / Redundancy: 11.1 % / Biso Wilson estimate: 11.47 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.025 / Rrim(I) all: 0.083 / Net I/σ(I): 20.3 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing |
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 57.84 Å2 / Biso mean: 18.7243 Å2 / Biso min: 0.52 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.227→48.991 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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