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- PDB-5v2u: Ethylene forming enzyme apo form -

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Basic information

Entry
Database: PDB / ID: 5v2u
TitleEthylene forming enzyme apo form
Components2-oxoglutarate-dependent ethylene/succinate-forming enzyme
KeywordsOXIDOREDUCTASE / alpha-Ketoglutaric acid / 2-Ketoglutaric acid / 2-Oxoglutaric acid / Oxoglutaric acid / 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
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: 2.058 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 / Category: pdbx_audit_support / Item: _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
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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


Theoretical massNumber of molelcules
Total (without water)40,1391
Polymers40,1391
Non-polymers00
Water5,008278
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.968, 86.833, 91.823
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: 40138.809 Da / Num. of mol.: 1 / Mutation: N-terminal fusion to SH
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.16 Å3/Da / Density % sol: 42.96 % / Mosaicity: 0.2 °
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.5 ul 72 mg/ml EFE (25 mM HEPES pH 8.0, 1 mM TCEP) was mixed with 0.5 ul reservoir solution. The sitting drop reservoir of 200 ul contained 0.2 M lithium chloride, 0.1 M Tris-HCl pH 8.0, ...Details: 0.5 ul 72 mg/ml EFE (25 mM HEPES pH 8.0, 1 mM TCEP) was mixed with 0.5 ul reservoir solution. The sitting drop reservoir of 200 ul contained 0.2 M lithium chloride, 0.1 M Tris-HCl pH 8.0, 20% w/v Polyethylene glycol 6,000. The crystal was direcly frozen.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.058→45.91 Å / Num. obs: 21539 / % possible obs: 98.1 % / Redundancy: 3.7 % / Biso Wilson estimate: 14.85 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.081 / Rrim(I) all: 0.164 / Net I/σ(I): 9.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) all% possible all
2.058-2.113.60.49616520.7780.2880.57798.2
8.97-45.9130.0520.9820.0360.06394.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.9 Å43.42 Å
Translation5.9 Å43.42 Å

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Processing

Software
NameVersionClassification
Aimless0.5.29data scaling
PHASER2.7.16phasing
PHENIX1.11.1-2575refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5V2T

5v2t


Resolution: 2.058→43.416 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 23.47
RfactorNum. reflection% reflection
Rfree0.2451 1025 4.81 %
Rwork0.1856 --
obs0.1883 19464 94.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 80.67 Å2 / Biso mean: 18.8089 Å2 / Biso min: 5.94 Å2
Refinement stepCycle: final / Resolution: 2.058→43.416 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2725 0 0 278 3003
Biso mean---22.15 -
Num. residues----344
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032818
X-RAY DIFFRACTIONf_angle_d0.6163830
X-RAY DIFFRACTIONf_chiral_restr0.042407
X-RAY DIFFRACTIONf_plane_restr0.004502
X-RAY DIFFRACTIONf_dihedral_angle_d2.3892322
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0577-2.11340.30641490.24672852300195
2.1134-2.17550.29381080.24412913302196
2.1755-2.24580.31511810.22422889307096
2.2458-2.3260.28551470.20782831297896
2.326-2.41910.28541390.21392953309295
2.4191-2.52920.29281500.21152819296994
2.5292-2.66260.27511530.20762866301995
2.6626-2.82940.27451630.19382847301095
2.8294-3.04780.27471630.19562843300694
3.0478-3.35440.23151390.17422797293694
3.3544-3.83950.18741110.14792857296894
3.8395-4.83630.13811330.13712818295193
4.8363-43.42610.23091370.16222771290892
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)
11.6486-0.0343-0.31651.1439-2.04224.83170.0571-0.33230.04020.1609-0.1603-0.0441-0.00110.44180.10660.1514-0.0037-0.00780.1867-0.00480.127126.1098-20.0853-18.6994
22.1279-0.3269-1.4160.6461.63224.3069-0.2149-0.269-0.2068-0.118-0.083-0.0715-0.00840.25180.28390.1660.0282-0.00990.08220.02020.105521.734-20.9136-21.3522
35.5171-5.4108-5.39042.00628.9157.9942-0.1758-0.0777-0.11210.1580.105-0.3880.07160.47630.04540.2355-0.06620.04720.21480.03650.195232.1395-0.4685-11.6908
40.79950.01230.28591.0906-0.47143.0515-0.1084-0.09280.02390.22570.06760.0132-0.16840.00950.0350.12330.01320.01780.0637-0.00450.091815.92399.0175-9.3293
53.06784.26993.40178.28425.87334.9743-0.09470.15520.2377-0.1840.02240.2356-0.17520.28120.07760.10420.02360.0070.11650.03290.11123.5878-4.0716-22.1652
60.62060.07810.6560.60240.30112.59960.0401-0.0938-0.03610.0064-0.00990.11680.0846-0.221-0.02980.07580.01070.01250.08880.00420.114114.1176-12.3211-10.2517
71.387-1.48440.54892.0599-0.45342.58530.1091-0.0847-0.1556-0.1503-0.0910.36870.227-0.4520.00060.1579-0.05630.00640.09990.02130.13666.915-4.6051-19.5555
85.71370.13762.87815.30831.07278.4162-0.18840.10620.41820.00930.08550.2669-0.6049-0.61010.10890.16050.05280.05980.2080.04970.17361.05479.8534-16.4145
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 16 )A-1 - 16
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 41 )A17 - 41
3X-RAY DIFFRACTION3chain 'A' and (resid 42 through 59 )A42 - 59
4X-RAY DIFFRACTION4chain 'A' and (resid 60 through 123 )A60 - 123
5X-RAY DIFFRACTION5chain 'A' and (resid 124 through 152 )A124 - 152
6X-RAY DIFFRACTION6chain 'A' and (resid 153 through 276 )A153 - 276
7X-RAY DIFFRACTION7chain 'A' and (resid 277 through 317 )A277 - 317
8X-RAY DIFFRACTION8chain 'A' and (resid 318 through 342 )A318 - 342

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