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- PDB-9scf: Fe(II)-2-oxoglutarate-dependent Pseudomonas savastanoi pv phaseol... -

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Basic information

Entry
Database: PDB / ID: 9scf
TitleFe(II)-2-oxoglutarate-dependent Pseudomonas savastanoi pv phaseolicola 1449B in complex with 2-oxoglutarate
Components2-oxoglutarate-dependent ethylene/succinate-forming enzyme
KeywordsOXIDOREDUCTASE / oxodoreductase / Iron
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
: / 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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsSun, Y. / Dhingra, S. / Allen, M. / Brewitz, L. / Schofield, C.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V003291/1 United Kingdom
CitationJournal: Chembiochem / Year: 2026
Title: Structural and Functional Validation of Pseudomonas Savastanoi Ethylene Forming Enzymes Reveals Flexibility in 2-Oxoglutarate Binding Mode and Conformation.
Authors: Sun, Y. / Dhingra, S. / Allen, M.D. / Cheng, E.S.Z. / Zhang, Z. / Schofield, C.J. / Brewitz, L.
History
DepositionAug 10, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 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)38,3113
Polymers38,1101
Non-polymers2012
Water5,080282
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.063, 56.063, 100.988
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Space group name HallP4cw
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: -x,-y,z+1/2

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Components

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


Mass: 38110.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas savastanoi (bacteria) / Gene: ALP21_100793 / Plasmid: pet28a-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): pLysY
References: UniProt: A0A7Z6Y5V5, 2-oxoglutarate dioxygenase (ethene-forming), 2-oxoglutarate/L-arginine monooxygenase/decarboxylase (succinate-forming)
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.08 Å3/Da / Density % sol: 40.93 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 0.03 M Citric acid, 0.07 M BIS-TRIS propane (pH 7.6), 20% w/v Polyethylene glycol (PEG) 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97628 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 24, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97628 Å / Relative weight: 1
ReflectionResolution: 1.65→56.08 Å / Num. obs: 37374 / % possible obs: 99.8 % / Redundancy: 11.5 % / Biso Wilson estimate: 20.86 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.031 / Rrim(I) all: 0.107 / Net I/σ(I): 10.7
Reflection shellResolution: 1.65→1.68 Å / Rmerge(I) obs: 1.587 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1740 / CC1/2: 0.867 / Rpim(I) all: 1.66 / Rrim(I) all: 0.483

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→39.64 Å / SU ML: 0.1953 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.5842
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1977 1921 5.17 %
Rwork0.1715 35235 -
obs0.1729 37156 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.92 Å2
Refinement stepCycle: LAST / Resolution: 1.65→39.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2664 0 11 282 2957
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00992775
X-RAY DIFFRACTIONf_angle_d1.06213770
X-RAY DIFFRACTIONf_chiral_restr0.0916396
X-RAY DIFFRACTIONf_plane_restr0.0094498
X-RAY DIFFRACTIONf_dihedral_angle_d15.85181023
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.690.32351170.30712425X-RAY DIFFRACTION96.95
1.69-1.740.30461170.28612508X-RAY DIFFRACTION98.65
1.74-1.790.29511760.26912475X-RAY DIFFRACTION99.21
1.79-1.850.30681380.23752489X-RAY DIFFRACTION99.28
1.85-1.910.2591530.21832493X-RAY DIFFRACTION98.99
1.91-1.990.2751410.20462514X-RAY DIFFRACTION99.29
1.99-2.080.24881310.20932525X-RAY DIFFRACTION99.81
2.08-2.190.22971370.19492528X-RAY DIFFRACTION99.81
2.19-2.330.20771300.19332555X-RAY DIFFRACTION99.89
2.33-2.510.19451250.16982537X-RAY DIFFRACTION99.92
2.51-2.760.22351420.1872520X-RAY DIFFRACTION99.89
2.76-3.160.22661430.17112537X-RAY DIFFRACTION100
3.16-3.980.15531340.14412558X-RAY DIFFRACTION99.96
3.98-39.640.13551370.13222571X-RAY DIFFRACTION99.89
Refinement TLS params.Method: refined / Origin x: -6.36975040715 Å / Origin y: -27.0599210482 Å / Origin z: 7.01924884708 Å
111213212223313233
T0.187180196457 Å2-0.0342589392197 Å2-0.00584252366241 Å2-0.227288863919 Å20.0172014475926 Å2--0.242878415629 Å2
L1.63117861769 °2-0.203104364668 °20.402847733593 °2-1.38079107219 °2-1.25832174764 °2--3.71655184046 °2
S-0.0090217288252 Å °0.0489574868716 Å °-0.0482747432671 Å °0.153031773086 Å °-0.06929259308 Å °-0.0869563026661 Å °-0.239572275193 Å °0.446207974997 Å °0.0230007315404 Å °
Refinement TLS groupSelection details: chain A

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