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- PDB-6vp5: Ethylene forming enzyme (EFE) D191E variant in complex with Fe(II... -

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Basic information

Entry
Database: PDB / ID: 6vp5
TitleEthylene forming enzyme (EFE) D191E variant in complex with Fe(II), L-arginine, and 2OG
Components2-oxoglutarate-dependent ethylene/succinate-forming enzyme
KeywordsOXIDOREDUCTASE / 2-oxo-glutarate / iron / reactant complex
Function / homology
Function and homology information


2-oxoglutarate oxygenase/decarboxylase (ethylene-forming) activity / 2-oxoglutarate dioxygenase (ethene-forming) / 2-oxoglutarate/L-arginine monooxygenase/decarboxylase (succinate-forming) / 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 / ARGININE / : / 2-oxoglutarate-dependent ethylene/succinate-forming enzyme
Similarity search - Component
Biological speciesPseudomonas savastanoi pv. phaseolicola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsDavis, K.M. / Copeland, R.A. / Boal, A.K.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM129460 United States
Department of Energy (DOE, United States) United States
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: An Iron(IV)-Oxo Intermediate Initiating l-Arginine Oxidation but Not Ethylene Production by the 2-Oxoglutarate-Dependent Oxygenase, Ethylene-Forming Enzyme.
Authors: Copeland, R.A. / Davis, K.M. / Shoda, T.K.C. / Blaesi, E.J. / Boal, A.K. / Krebs, C. / Bollinger Jr., J.M.
History
DepositionFeb 1, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Feb 24, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
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)160,16217
Polymers158,3714
Non-polymers1,79113
Water22,5371251
1
A: 2-oxoglutarate-dependent ethylene/succinate-forming enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9704
Polymers39,5931
Non-polymers3773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 2-oxoglutarate-dependent ethylene/succinate-forming enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9704
Polymers39,5931
Non-polymers3773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 2-oxoglutarate-dependent ethylene/succinate-forming enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9704
Polymers39,5931
Non-polymers3773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 2-oxoglutarate-dependent ethylene/succinate-forming enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2525
Polymers39,5931
Non-polymers6594
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.542, 78.500, 195.492
Angle α, β, γ (deg.)90.000, 92.342, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 39592.645 Da / Num. of mol.: 4 / Mutation: D191E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas savastanoi pv. phaseolicola (bacteria)
Gene: efe / Production host: Escherichia coli (E. coli)
References: UniProt: P32021, 2-oxoglutarate dioxygenase (ethene-forming), 2-oxoglutarate/L-arginine monooxygenase/decarboxylase (succinate-forming)

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Non-polymers , 5 types, 1264 molecules

#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical
ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H15N4O2
#5: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1251 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.4 Å3/Da / Density % sol: 48.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris propane, 0.1-0.2 M sodium chloride, 24-30% PEG6000
PH range: 6.4-6.7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 30, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.97→49.52 Å / Num. obs: 105982 / % possible obs: 99.21 % / Redundancy: 7.5 % / Biso Wilson estimate: 16.6 Å2 / Rpim(I) all: 0.04034 / Net I/σ(I): 16.65
Reflection shellResolution: 1.97→2.04 Å / Num. unique obs: 9842 / Rpim(I) all: 0.2801

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.15.2_3472refinement
Cootmodel building
PHENIX1.15.2_3472phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5LSQ

5lsq


Resolution: 1.97→49.52 Å / SU ML: 0.1759 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.9225
RfactorNum. reflection% reflection
Rfree0.2067 1592 1.51 %
Rwork0.1735 --
obs0.174 105151 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 19.51 Å2
Refinement stepCycle: LAST / Resolution: 1.97→49.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10530 0 111 1251 11892
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003511032
X-RAY DIFFRACTIONf_angle_d0.633615015
X-RAY DIFFRACTIONf_chiral_restr0.04281604
X-RAY DIFFRACTIONf_plane_restr0.00381978
X-RAY DIFFRACTIONf_dihedral_angle_d20.8934006
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.030.24211310.23018766X-RAY DIFFRACTION93.26
2.03-2.110.27531420.21639425X-RAY DIFFRACTION99.46
2.11-2.190.2331520.20049379X-RAY DIFFRACTION99.97
2.19-2.290.24321420.1989463X-RAY DIFFRACTION99.98
2.29-2.410.24871480.19279440X-RAY DIFFRACTION99.98
2.41-2.560.24761440.18429456X-RAY DIFFRACTION99.95
2.56-2.760.24941420.1829510X-RAY DIFFRACTION99.78
2.76-3.040.21151480.17679417X-RAY DIFFRACTION99.73
3.04-3.480.18561500.16129483X-RAY DIFFRACTION99.71
3.48-4.380.15731480.13749539X-RAY DIFFRACTION99.78
4.38-49.520.15871450.15349681X-RAY DIFFRACTION99.72

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