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- PDB-5v2y: Ethylene forming enzyme in complex with manganese, 2-oxoglutarate... -

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Basic information

Entry
Database: PDB / ID: 5v2y
TitleEthylene forming enzyme in complex with manganese, 2-oxoglutarate and L-arginine
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-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 / molecular replacement / Resolution: 1.428 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

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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)40,0934
Polymers39,7171
Non-polymers3763
Water6,359353
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.479, 82.116, 87.593
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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2
#4: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / 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: 43.96 % / Mosaicity: 0.14 °
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 ul 64 mg/ml EFE (+4 mM manganese chloride, 25 mM HEPES pH 8.0, 1 mM TCEP, 2.5 mM 2-oxoglutarate, 2.5 mM L-arginine) was mixed with 0.2 ul reservoir solution. The sitting drop reservoir ...Details: 0.2 ul 64 mg/ml EFE (+4 mM manganese chloride, 25 mM HEPES pH 8.0, 1 mM TCEP, 2.5 mM 2-oxoglutarate, 2.5 mM L-arginine) was mixed with 0.2 ul reservoir solution. The sitting drop reservoir of 50 ul contained 0.2 M sodium chloride, 0.1 M BIS-TRIS pH 6.5, 25% w/v Polyethylene glycol 3,350. 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-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.428→43.8 Å / Num. obs: 65410 / % possible obs: 99.7 % / Redundancy: 5.8 % / Biso Wilson estimate: 12.11 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.029 / Rrim(I) all: 0.072 / Net I/σ(I): 15.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) all% possible all
1.43-1.453.90.60231590.7730.3410.69596.3
7.69-43.84.80.0350.9980.0180.0496.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.98 Å43.8 Å
Translation5.98 Å43.8 Å

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Processing

Software
NameVersionClassification
Aimless0.5.31data 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: 1.428→43.797 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 15.05
RfactorNum. reflection% reflection
Rfree0.1607 3234 4.95 %
Rwork0.132 --
obs0.1334 62374 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 60.01 Å2 / Biso mean: 18.4836 Å2 / Biso min: 7.76 Å2
Refinement stepCycle: final / Resolution: 1.428→43.797 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2715 0 42 353 3110
Biso mean--15.52 29.37 -
Num. residues----341
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072895
X-RAY DIFFRACTIONf_angle_d0.9493936
X-RAY DIFFRACTIONf_chiral_restr0.075413
X-RAY DIFFRACTIONf_plane_restr0.007523
X-RAY DIFFRACTIONf_dihedral_angle_d14.8641072
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4285-1.44470.27132340.24873560379491
1.4447-1.46170.26242240.215439384162100
1.4617-1.47950.24652160.202439214137100
1.4795-1.49830.22392000.179439914191100
1.4983-1.5180.19141810.17140264207100
1.518-1.53880.19042270.161539244151100
1.5388-1.56080.21532050.152640264231100
1.5608-1.5840.17611840.144139334117100
1.584-1.60880.20061860.139539884174100
1.6088-1.63520.1811830.13339724155100
1.6352-1.66340.15361860.1340014187100
1.6634-1.69360.17212120.12639494161100
1.6936-1.72620.14972060.118339904196100
1.7262-1.76140.17852150.11939484163100
1.7614-1.79970.14971840.110840134197100
1.7997-1.84160.15422300.112438994129100
1.8416-1.88770.13951830.110639874170100
1.8877-1.93870.16811870.111740124199100
1.9387-1.99570.14221860.109539914177100
1.9957-2.06020.14262110.109239334144100
2.0602-2.13380.1242080.111639454153100
2.1338-2.21920.15272000.108440154215100
2.2192-2.32020.13251780.107639834161100
2.3202-2.44250.13032130.113539784191100
2.4425-2.59550.14132180.115239314149100
2.5955-2.79590.14662150.127339494164100
2.7959-3.07720.17782460.136939534199100
3.0772-3.52230.14742280.135439384166100
3.5223-4.43710.14332130.1339484161100
4.4371-43.81710.18612130.16683935414899

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