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- PDB-5v31: Ethylene forming enzyme in complex with manganese and L-arginine -

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Basic information

Entry
Database: PDB / ID: 5v31
TitleEthylene forming enzyme in complex with manganese and L-arginine
Components2-oxoglutarate-dependent ethylene/succinate-forming enzyme
KeywordsOXIDOREDUCTASE / ethylene biosynthesis
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
ARGININE / : / 2-oxoglutarate-dependent ethylene/succinate-forming enzyme
Similarity search - Component
Biological speciesPseudomonas savastanoi pv. phaseolicola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.45 Å
AuthorsFellner, M. / Martinez, S. / Hu, J. / Hausinger, R.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM063584 United States
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: Structures and Mechanisms of the Non-Heme Fe(II)- and 2-Oxoglutarate-Dependent Ethylene-Forming Enzyme: Substrate Binding Creates a Twist.
Authors: Martinez, S. / Fellner, M. / Herr, C.Q. / Ritchie, A. / Hu, J. / Hausinger, R.P.
History
DepositionMar 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Data collection / Refinement description
Category: diffrn_detector / pdbx_audit_support / software
Item: _diffrn_detector.detector / _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)39,9473
Polymers39,7171
Non-polymers2302
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.630, 81.910, 87.160
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#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)


Mass: 39716.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas savastanoi pv. phaseolicola (bacteria)
Gene: efe / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold (DE3)
References: UniProt: P32021, 2-oxoglutarate dioxygenase (ethene-forming), EC: 1.14.11.34
#2: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O

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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: 2.19 Å3/Da / Density % sol: 43.72 % / Mosaicity: 0.56 °
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 ul 64 mg/ml EFE (+4 mM manganese chloride, 25 mM HEPES pH 8.0, 1 mM TCEP, +2.5 mM L-arginine) was mixed with 0.2 ul reservoir solution. The sitting drop reservoir of 50 ul contained 0.1 ...Details: 0.2 ul 64 mg/ml EFE (+4 mM manganese chloride, 25 mM HEPES pH 8.0, 1 mM TCEP, +2.5 mM L-arginine) was mixed with 0.2 ul reservoir solution. The sitting drop reservoir of 50 ul contained 0.1 M HEPES/ Sodium hydroxide pH 7.5, 25% w/v Polyethylene glycol 10,000. The crystal was soaked for about a minute in 25% w/v Polyethylene glycol 400, 75% reservoir solution before freezing it.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.1272 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1272 Å / Relative weight: 1
ReflectionResolution: 2.45→87.16 Å / Num. obs: 12891 / % possible obs: 97.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 20.92 Å2 / CC1/2: 0.972 / Rmerge(I) obs: 0.18 / Rpim(I) all: 0.106 / Rrim(I) all: 0.21 / Net I/σ(I): 5.4 / Num. measured all: 45124 / Scaling rejects: 16
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) all% possible all
2.45-2.553.60.56514510.7180.3340.6698
8.83-87.163.70.0850.9840.0490.09891.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.8 Å43.58 Å
Translation5.8 Å43.58 Å

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.5.31data scaling
PHASER2.7.16phasing
PHENIX1.11.1-2575refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5V2T

5v2t


Resolution: 2.45→43.58 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 24.14
RfactorNum. reflection% reflection
Rfree0.2468 559 4.37 %
Rwork0.1798 --
obs0.1828 11324 91.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 78.54 Å2 / Biso mean: 25.031 Å2 / Biso min: 9.39 Å2
Refinement stepCycle: final / Resolution: 2.45→43.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2699 0 13 128 2840
Biso mean--30.28 25.51 -
Num. residues----340
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162799
X-RAY DIFFRACTIONf_angle_d0.9153793
X-RAY DIFFRACTIONf_chiral_restr0.05403
X-RAY DIFFRACTIONf_plane_restr0.006496
X-RAY DIFFRACTIONf_dihedral_angle_d2.8942311
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4502-2.57940.31081260.23893171329793
2.5794-2.7410.27831390.23123091323092
2.741-2.95260.29181320.21482950308288
2.9526-3.24960.28041450.1993213335895
3.2496-3.71960.25551210.16353193331494
3.7196-4.68540.22071860.13453046323292
4.6854-43.58690.18861400.16142996313689
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)
11.943-0.39921.23252.35771.342.17570.03550.10090.3055-0.30070.0242-0.1965-0.41740.0148-0.05060.19-0.02360.00830.10710.03410.1559-11.9972.211-11.973
20.9280.38570.23440.98160.00421.30870.050.023-0.03050.0192-0.0048-0.0871-0.03890.0772-0.03070.10110.0115-0.00250.1426-0.01990.1336-0.0121.94514.927
33.57223.75686.35464.97137.13452.00330.0377-0.25040.24830.1769-0.31640.18980.19-0.47560.27410.2157-0.03840.06440.1974-0.0010.1795-12.3313.2814.471
41.09460.12730.22481.188-0.14041.81720.02160.0417-0.168-0.014-0.0007-0.19880.19790.2191-0.00920.13910.0247-0.00450.1719-0.03570.14180.571-6.7531.072
57.75334.9594-3.31787.35063.505820.05710.0805-0.1424-0.1626-0.0902-0.10760.6190.30880.03280.52050.0857-0.01820.2721-0.11850.27186.308-5.8224.854
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 3:41 )A3 - 41
2X-RAY DIFFRACTION2( CHAIN A AND RESID 42:123 )A42 - 123
3X-RAY DIFFRACTION3( CHAIN A AND RESID 124:151 )A124 - 151
4X-RAY DIFFRACTION4( CHAIN A AND RESID 152:342 )A152 - 342
5X-RAY DIFFRACTION5( CHAIN A AND RESID 401:401 )A401

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