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- PDB-9eis: Ethylene forming enzyme in complex with manganese and 2-oxoglutar... -

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Basic information

Entry
Database: PDB / ID: 9eis
TitleEthylene forming enzyme in complex with manganese and 2-oxoglutarate from Penicillium digitatum
Components2-oxoglutarate-dependent ethylene/succinate-forming enzyme
KeywordsOXIDOREDUCTASE / 2-oxoglutarate-dependent ethylene/succinate-forming enzyme
Function / homology
Function and homology information


small molecule biosynthetic process / oxidoreductase 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 speciesPenicillium digitatum Pd1 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsChatterjee, S. / Rankin, J.A. / Farrugia, M.A. / Hu, J. / Hausinger, R.P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1904295 United States
National Science Foundation (NSF, United States)2203472 United States
CitationJournal: Biochemistry / Year: 2025
Title: Biochemical, Structural, and Conformational Characterization of a Fungal Ethylene-Forming Enzyme.
Authors: Chatterjee, S. / Rankin, J.A. / Farrugia, M.A. / J S Rifayee, S.B. / Christov, C.Z. / Hu, J. / Hausinger, R.P.
History
DepositionNov 26, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release
Revision 1.1May 14, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)183,87213
Polymers183,2274
Non-polymers6459
Water5,621312
1
A: 2-oxoglutarate-dependent ethylene/succinate-forming enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0083
Polymers45,8071
Non-polymers2012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 2-oxoglutarate-dependent ethylene/succinate-forming enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8973
Polymers45,8071
Non-polymers902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 2-oxoglutarate-dependent ethylene/succinate-forming enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0434
Polymers45,8071
Non-polymers2363
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: 2-oxoglutarate-dependent ethylene/succinate-forming enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9243
Polymers45,8071
Non-polymers1172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.159, 117.400, 140.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
2-oxoglutarate-dependent ethylene/succinate-forming enzyme


Mass: 45806.812 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium digitatum Pd1 (fungus) / Gene: Pdw03_5776 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A7T7BQH3

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Non-polymers , 5 types, 321 molecules

#2: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.35 Å3/Da / Density % sol: 47.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 10 % PEG 8000, 100 mM imidazole-HCl (pH 8.0), and 200 mM calcium acetate and soaked overnight with 1 mM MnCl2 and 2OG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.127 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 2.8→90.1 Å / Num. obs: 43000 / % possible obs: 99.5 % / Redundancy: 6.7 % / CC1/2: 0.949 / Net I/σ(I): 5.5
Reflection shellResolution: 2.8→2.91 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4494 / CC1/2: 0.352

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→22.85 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2865 2082 4.86 %
Rwork0.2499 --
obs0.2517 42805 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→22.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9916 0 30 312 10258
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01910233
X-RAY DIFFRACTIONf_angle_d1.5613945
X-RAY DIFFRACTIONf_dihedral_angle_d15.2843672
X-RAY DIFFRACTIONf_chiral_restr0.0961518
X-RAY DIFFRACTIONf_plane_restr0.0091835
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.860.35061300.32432710X-RAY DIFFRACTION100
2.87-2.940.31621430.31822662X-RAY DIFFRACTION100
2.94-3.020.29451390.30192703X-RAY DIFFRACTION100
3.02-3.10.30361360.30332668X-RAY DIFFRACTION100
3.1-3.20.36421500.30692696X-RAY DIFFRACTION100
3.2-3.320.33141380.29782680X-RAY DIFFRACTION100
3.32-3.450.28491400.26812722X-RAY DIFFRACTION100
3.45-3.610.27521370.24392582X-RAY DIFFRACTION95
3.61-3.80.24361330.24432730X-RAY DIFFRACTION100
3.8-4.030.31781290.23552735X-RAY DIFFRACTION100
4.03-4.340.24771330.21282744X-RAY DIFFRACTION100
4.34-4.780.26431340.20332744X-RAY DIFFRACTION100
4.78-5.460.25251460.21882760X-RAY DIFFRACTION100
5.46-6.850.30221560.24862708X-RAY DIFFRACTION98
6.85-22.850.27821380.23262879X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8525-0.1179-1.12094.11582.73863.8133-0.64150.19480.2943-0.77220.1594-0.18310.0108-0.06640.48060.89280.2720.16750.52050.06380.6946-33.6467-7.1957-25.4939
20.5661-0.1202-0.31690.3655-0.02821.04270.2322-0.00860.23120.43160.29160.1737-0.688-0.5231-0.14791.3470.86520.33191.23430.24620.0462-21.7169-31.1149-23.5254
30.260.3132-0.27749.44755.37114.04210.04450.19310.24220.45240.6571-0.274-0.36560.1735-0.64881.07750.56110.18730.95470.0890.4774-25.0677-18.9473-17.1136
47.03034.26622.84845.9461.69363.61830.3065-0.8424-0.67350.3331-0.24380.4185-0.1877-0.5007-0.07280.64140.38810.03820.90610.19940.8862-39.7365-24.0054-25.4151
51.1039-0.47470.12941.9664-0.63690.55570.16140.6191-0.07780.5112-0.08540.57320.14150.133-0.07090.74160.30690.13650.89260.1910.5603-36.6478-21.9703-20.6398
64.3766-0.27140.90085.52790.73942.51710.13430.00610.68110.4054-0.46770.8995-0.05780.21270.3570.95150.31060.15520.53510.06520.8443-28.527-14.2429-5.1282
70.188-0.0133-0.37087.93622.74611.6343-0.1609-0.32620.01760.25630.15590.9775-0.11370.03090.02110.47820.15630.16280.63740.22220.5138-29.393-28.5617-7.094
81.0710.9954-1.11452.2532-2.19532.1764-0.2301-0.5749-0.06730.3318-0.1367-0.1181-0.3109-0.01060.3250.74530.1810.07721.1890.10030.454-22.6218-35.7373-4.2466
91.6404-0.06930.16051.7028-0.05190.84320.18630.1657-0.2165-0.8014-0.1090.3023-0.44780.8023-0.01040.4199-0.24180.10960.42140.02750.1358-1.5554-4.9454-58.332
101.01631.01680.85532.32190.4151.7071-0.0810.20970.0373-0.41780.1363-0.0146-0.55440.7098-0.06560.4037-0.2044-0.00950.41470.07110.21992.92050.6031-50.828
111.5169-0.03680.78131.70461.43834.17050.0198-0.0352-0.11680.00790.09130.01140.15740.3393-0.09590.2342-0.0390.02320.18730.02790.20182.7568-6.0733-43.6117
122.56790.41470.64161.5423-0.42071.37310.03460.7260.1432-0.1858-0.0172-0.1291-0.11140.14590.03180.35920.03120.15150.43250.09870.306621.9261-46.412-81.5774
132.88960.6733-1.39691.77560.84334.05720.03710.54150.1572-0.24660.1426-0.06680.0135-0.3283-0.1070.31430.0309-0.00320.29140.04790.15410.9069-60.2704-73.6247
142.66351.343-1.28760.7266-0.89131.84780.0549-0.1402-0.0390.0339-0.0072-0.0622-0.15260.0511-0.10180.29320.07030.00620.203-0.02480.261412.4823-56.0157-64.1254
152.0760.42550.1241.9284-0.73422.41190.02130.63590.2461-0.09350.43210.7274-0.0328-0.9148-0.35830.30320.06070.04630.64280.19930.46794.0181-48.4664-81.2767
162.49350.6146-1.2661.592-0.13252.72520.20790.13920.41560.0954-0.00120.0915-0.4943-0.1569-0.17830.30790.06290.02880.22050.05140.2888.6939-44.3027-66.7026
171.3356-0.8012-0.5992.74670.15371.48630.1490.1889-0.1193-0.4051-0.054-0.15580.1190.1811-0.09650.3079-0.0075-0.07140.3428-0.02030.213514.6385-20.9348-23.3785
183.26460.4464-1.55526.0389-0.02156.58410.6186-0.48830.24840.6972-0.1109-1.3959-1.33290.796-0.51490.55530.0763-0.08710.6976-0.15040.623629.7196-14.3127-17.9543
191.568-0.318-0.10822.57010.47951.84650.13990.0275-0.2241-0.04120.0517-0.17790.13230.195-0.16670.19580.0386-0.08320.2645-0.0220.277220.1984-26.1721-15.6647
201.25790.1549-1.4411.67760.18951.70220.0108-0.1131-0.1360.0801-0.07960.1481-0.2573-0.39230.03660.60610.45030.0931.33820.21240.8421-40.1015-15.6332-31.5875
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'D' and (resid 74 through 98 )
2X-RAY DIFFRACTION2chain 'D' and (resid 99 through 208 )
3X-RAY DIFFRACTION3chain 'D' and (resid 209 through 232 )
4X-RAY DIFFRACTION4chain 'D' and (resid 233 through 311 )
5X-RAY DIFFRACTION5chain 'D' and (resid 312 through 343 )
6X-RAY DIFFRACTION6chain 'D' and (resid 344 through 365 )
7X-RAY DIFFRACTION7chain 'D' and (resid 366 through 380 )
8X-RAY DIFFRACTION8chain 'D' and (resid 381 through 407 )
9X-RAY DIFFRACTION9chain 'A' and (resid 46 through 133 )
10X-RAY DIFFRACTION10chain 'A' and (resid 134 through 271 )
11X-RAY DIFFRACTION11chain 'A' and (resid 272 through 407 )
12X-RAY DIFFRACTION12chain 'B' and (resid 48 through 98 )
13X-RAY DIFFRACTION13chain 'B' and (resid 99 through 155 )
14X-RAY DIFFRACTION14chain 'B' and (resid 156 through 232 )
15X-RAY DIFFRACTION15chain 'B' and (resid 233 through 270 )
16X-RAY DIFFRACTION16chain 'B' and (resid 271 through 407 )
17X-RAY DIFFRACTION17chain 'C' and (resid 46 through 232 )
18X-RAY DIFFRACTION18chain 'C' and (resid 233 through 256 )
19X-RAY DIFFRACTION19chain 'C' and (resid 257 through 407 )
20X-RAY DIFFRACTION20chain 'D' and (resid 45 through 73 )

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