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- PDB-5vkb: Ethylene forming enzyme in complex with manganese, 2-oxoglutarate... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5vkb | ||||||
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Title | Ethylene forming enzyme in complex with manganese, 2-oxoglutarate and argininamide | ||||||
![]() | 2-oxoglutarate-dependent ethylene/succinate-forming enzyme | ||||||
![]() | OXIDOREDUCTASE / 2-oxoglutarate / argininamide | ||||||
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. | ||||||
![]() | ![]() 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 | ![]() | 230.4 KB | Display | ![]() |
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PDB format | ![]() | 185.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.7 KB | Display | ![]() |
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Full document | ![]() | 457.8 KB | Display | |
Data in XML | ![]() | 19.7 KB | Display | |
Data in CIF | ![]() | 31.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5v2tC ![]() 5v2uC ![]() 5v2vC ![]() 5v2xC ![]() 5v2yC ![]() 5v2zSC ![]() 5v31C ![]() 5v32C ![]() 5v34C ![]() 5vkaC C: citing same article ( S: Starting model for refinement |
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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-AKG / |
#4: Chemical | ChemComp-AAR / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.85 % / Mosaicity: 0.07 ° |
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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 argininamide, 0.2 uL of 100 mM 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 argininamide, 0.2 uL of 100 mM 2-oxoglutarate. 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 Polyethylene glycol 400, 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: 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: 1.139→48.48 Å / Num. obs: 127532 / % possible obs: 99.6 % / Redundancy: 8.4 % / Biso Wilson estimate: 10.59 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.032 / Rrim(I) all: 0.094 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 1.139→1.16 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.912 / Num. unique obs: 5998 / CC1/2: 0.747 / Rpim(I) all: 0.422 / Rrim(I) all: 1.009 / % possible all: 95.4 |
-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5V2Z Resolution: 1.139→38.679 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 17.05
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 70.29 Å2 / Biso mean: 19.2159 Å2 / Biso min: 6.85 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.139→38.679 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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