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- PDB-5lun: Ethylene Forming Enzyme from Pseudomonas syringae pv. phaseolicol... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5lun | ||||||
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Title | Ethylene Forming Enzyme from Pseudomonas syringae pv. phaseolicola - P1 ultra-high resolution crystal form in complex with iron, N-oxalylglycine and arginine | ||||||
![]() | 2-oxoglutarate-dependent ethylene/succinate-forming enzyme | ||||||
![]() | OXIDOREDUCTASE / 2-oxoglutarate and ferrous iron dependent oxygenase / ethylene forming / double stranded beta helix | ||||||
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 | ![]() ![]() ![]() ![]() | ||||||
![]() | McDonough, M.A. / Zhang, Z. / Schofield, C.J. | ||||||
![]() | ![]() Title: Structural and stereoelectronic insights into oxygenase-catalyzed formation of ethylene from 2-oxoglutarate. Authors: Zhang, Z. / Smart, T.J. / Choi, H. / Hardy, F. / Lohans, C.T. / Abboud, M.I. / Richardson, M.S.W. / Paton, R.S. / McDonough, M.A. / Schofield, C.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 607.5 KB | Display | ![]() |
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PDB format | ![]() | 491.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 499 KB | Display | ![]() |
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Full document | ![]() | 510.2 KB | Display | |
Data in XML | ![]() | 72.2 KB | Display | |
Data in CIF | ![]() | 111.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5lsqSC ![]() 5mofC S: Starting model for refinement 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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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 39632.602 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: efe / Plasmid: pColdI / Production host: ![]() ![]() References: UniProt: P32021, 2-oxoglutarate dioxygenase (ethene-forming), EC: 1.14.11.34 |
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-Non-polymers , 5 types, 2065 molecules ![](data/chem/img/FE.gif)
![](data/chem/img/OGA.gif)
![](data/chem/img/ARG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/OGA.gif)
![](data/chem/img/ARG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FE / #3: Chemical | ChemComp-OGA / #4: Chemical | ChemComp-ARG / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.38 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 20% polyethylene glycol, 0.1 M Tris, 0.2 M sodium chloride, 0.01 M N-oxalylglycine, 0.02 M L-Arginine, protein concentration 15mg/mL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 25, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.08→77.6 Å / Num. obs: 584165 / % possible obs: 93 % / Redundancy: 3.5 % / Biso Wilson estimate: 11.557 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.053 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 1.08→1.12 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.822 / Mean I/σ(I) obs: 1.4 / CC1/2: 0.701 / % possible all: 89.3 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5LSQ Resolution: 1.08→77.597 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 26.14
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 75.14 Å2 / Biso mean: 21.1423 Å2 / Biso min: 6.3 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.08→77.597 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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