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- PDB-22pe: Ethylene Forming Enzyme in complex with 2-oxoglutarate -

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Basic information

Entry
Database: PDB / ID: 22pe
TitleEthylene Forming Enzyme in complex with 2-oxoglutarate
Components2-oxoglutarate-dependent ethylene/succinate-forming enzyme
KeywordsOXIDOREDUCTASE / complex / ethylene forming enzyme
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
Similarity search - Function
Non-haem dioxygenase N-terminal domain / non-haem dioxygenase in morphine synthesis N-terminal / Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Isopenicillin N synthase-like superfamily / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile.
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / : / 2-oxoglutarate-dependent ethylene/succinate-forming enzyme
Similarity search - Component
Biological speciesPseudomonas savastanoi pv. phaseolicola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsZhou, J.H. / Wang, M.Y.
Funding support China, 1items
OrganizationGrant numberCountry
Not funded China
CitationJournal: Eng Microbiol / Year: 2026
Title: Structure-guided surface engineering to improve the catalytic activity of ethylene-forming enzyme.
Authors: Wang, M. / Shen, Z. / Wu, L. / Huang, W. / Zhou, J. / Gu, Y.
History
DepositionJan 19, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 9, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-oxoglutarate-dependent ethylene/succinate-forming enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6063
Polymers39,4041
Non-polymers2022
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-10 kcal/mol
Surface area15400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.366, 97.751, 98.246
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein 2-oxoglutarate-dependent ethylene/succinate-forming enzyme / EFE / Ethylene-forming enzyme / 2-oxoglutarate dioxygenase (ethylene-forming) / 2-oxoglutarate/L- ...EFE / Ethylene-forming enzyme / 2-oxoglutarate dioxygenase (ethylene-forming) / 2-oxoglutarate/L-arginine monooxygenase/decarboxylase (succinate-forming)


Mass: 39404.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas savastanoi pv. phaseolicola (bacteria)
Gene: efe / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P32021, 2-oxoglutarate dioxygenase (ethene-forming), 2-oxoglutarate/L-arginine monooxygenase/decarboxylase (succinate-forming)
#2: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M sodium cacodylate pH 6.5, 25% (w/v) polyethylene glycol (PEG) 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9779 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9779 Å / Relative weight: 1
ReflectionResolution: 1.66→48.88 Å / Num. obs: 45253 / % possible obs: 99.6 % / Redundancy: 9.7 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.041 / Net I/σ(I): 16.97
Reflection shellResolution: 1.66→1.7 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.822 / Mean I/σ(I) obs: 1.63 / Num. unique obs: 2109 / CC1/2: 0.626 / Rpim(I) all: 0.362 / % possible all: 95.4

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.66→48.88 Å / SU ML: 0.1695 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.2447
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1929 2065 4.75 %
Rwork0.164 41363 -
obs0.1654 43428 95.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.15 Å2
Refinement stepCycle: LAST / Resolution: 1.66→48.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2722 0 11 274 3007
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01472907
X-RAY DIFFRACTIONf_angle_d1.25373968
X-RAY DIFFRACTIONf_chiral_restr0.0859422
X-RAY DIFFRACTIONf_plane_restr0.0137523
X-RAY DIFFRACTIONf_dihedral_angle_d13.86511098
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.70.32251110.26911766X-RAY DIFFRACTION62.75
1.7-1.740.28871100.22782306X-RAY DIFFRACTION80.75
1.74-1.790.21891200.2022577X-RAY DIFFRACTION90.44
1.79-1.840.23621510.18112766X-RAY DIFFRACTION96.85
1.84-1.90.2171630.17992837X-RAY DIFFRACTION99.3
1.9-1.970.21611570.18762842X-RAY DIFFRACTION99.9
1.97-2.050.21411250.16752909X-RAY DIFFRACTION100
2.05-2.140.19961450.15532852X-RAY DIFFRACTION99.97
2.14-2.250.19891690.15412848X-RAY DIFFRACTION100
2.25-2.390.1961320.15962897X-RAY DIFFRACTION99.97
2.39-2.580.17771100.15792943X-RAY DIFFRACTION99.97
2.58-2.840.19031710.16992862X-RAY DIFFRACTION100
2.84-3.250.21811190.16912931X-RAY DIFFRACTION99.9
3.25-4.090.15641420.14442955X-RAY DIFFRACTION99.87
4.09-48.880.15261400.14713072X-RAY DIFFRACTION99.91

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