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- PDB-5mof: Ethylene Forming Enzyme from Pseudomonas syringae pv. phaseolicol... -

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Basic information

Entry
Database: PDB / ID: 5mof
TitleEthylene Forming Enzyme from Pseudomonas syringae pv. phaseolicola - I222 crystal form in complex with manganese and 2-oxoglutarate
Components2-oxoglutarate-dependent ethylene/succinate-forming enzyme
KeywordsOXIDOREDUCTASE / 2-oxoglutarate and ferrous iron dependent oxygenase / ethylene forming / double stranded beta helix
Function / homology
Function and homology information


2-oxoglutarate dioxygenase (ethene-forming) / 2-oxoglutarate/L-arginine monooxygenase/decarboxylase (succinate-forming) / 2-oxoglutarate oxygenase/decarboxylase (ethylene-forming) activity / 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 / : / 2-oxoglutarate-dependent ethylene/succinate-forming enzyme
Similarity search - Component
Biological speciesPseudomonas savastanoi pv. phaseolicola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.45 Å
AuthorsMcDonough, M.A. / Zhang, Z. / Schofield, C.J.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structural and stereoelectronic insights into oxygenase-catalyzed formation of ethylene from 2-oxoglutarate.
Authors: Zhang, Z. / Smart, T.J. / Choi, H. / Hardy, F. / Lohans, C.T. / Abboud, M.I. / Richardson, M.S.W. / Paton, R.S. / McDonough, M.A. / Schofield, C.J.
History
DepositionDec 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
Revision 1.2May 10, 2017Group: Database references
Revision 2.0Jan 17, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)41,3228
Polymers40,7001
Non-polymers6227
Water8,413467
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.484, 97.850, 98.094
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-949-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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: 40699.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas savastanoi pv. phaseolicola (bacteria)
Gene: efe
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P32021, 2-oxoglutarate dioxygenase (ethene-forming), EC: 1.14.11.34

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Non-polymers , 5 types, 474 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O5
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 467 / 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: 2.34 Å3/Da / Density % sol: 47.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 17-20% PEG 3350, 100mM Bis-Tris Phosphate, 100mM Sodium potassium phosphate, 3mM manganese chloride, 10mM 2-oxoglutarate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9796 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.45→69.28 Å / Num. obs: 67866 / % possible obs: 100 % / Redundancy: 6.3 % / Biso Wilson estimate: 11.68 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.047 / Rrim(I) all: 0.12 / Net I/σ(I): 10.8 / Num. measured all: 430728 / Scaling rejects: 43
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.45-1.546.11.52120.5921100
4.35-69.286.40.0330.9951100

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Processing

Software
NameVersionClassification
Aimless0.5.1data scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5LUN

5lun


Resolution: 1.45→69.277 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 20.67
RfactorNum. reflection% reflection
Rfree0.1894 3369 4.98 %
Rwork0.1717 --
obs0.1726 67710 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 61.56 Å2 / Biso mean: 18.0431 Å2 / Biso min: 7.12 Å2
Refinement stepCycle: final / Resolution: 1.45→69.277 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2711 0 31 475 3217
Biso mean--27.9 29.27 -
Num. residues----343
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042969
X-RAY DIFFRACTIONf_angle_d0.7274051
X-RAY DIFFRACTIONf_chiral_restr0.064426
X-RAY DIFFRACTIONf_plane_restr0.005536
X-RAY DIFFRACTIONf_dihedral_angle_d13.1381113
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.45-1.47070.36511320.32962615274799
1.4707-1.49270.31491430.3222612275599
1.4927-1.5160.31631640.31092634279899
1.516-1.54090.3051200.29152676279699
1.5409-1.56740.29631210.27892666278799
1.5674-1.59590.30671350.270826562791100
1.5959-1.62660.27321420.250926482790100
1.6266-1.65980.24181390.243926632802100
1.6598-1.69590.25551600.232726262786100
1.6959-1.73540.27021490.217226532802100
1.7354-1.77880.2311320.203127132845100
1.7788-1.82690.21751340.191326232757100
1.8269-1.88070.16681530.172426752828100
1.8807-1.94140.19951240.16726902814100
1.9414-2.01080.17761340.163526672801100
2.0108-2.09130.18151530.149626802833100
2.0913-2.18640.17281370.141526832820100
2.1864-2.30170.15661330.138726962829100
2.3017-2.44590.16731330.131127022835100
2.4459-2.63480.1481160.135327482864100
2.6348-2.90.15051620.142926742836100
2.9-3.31960.17911510.146127432894100
3.3196-4.18230.14731270.126927572884100
4.1823-69.35570.15111750.161228413016100
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)
13.20080.12660.18374.2507-0.45981.2714-0.0589-0.14720.16840.17740.04290.089-0.1598-0.11080.01060.10020.02040.00470.0836-0.0430.075715.364648.448427.5565
20.11650.18460.35411.90550.22521.85520.0175-0.0499-0.07220.04660.01190.0010.17540.0272-0.00330.0655-0.0151-0.01360.10610.03030.115212.678120.307519.318
30.32320.22660.02631.01810.18570.3745-0.03080.02620.0405-0.0660.01490.03-0.0372-0.01880.02060.08-0.0026-0.01460.08560.01340.081712.803133.851112.1566
40.4550.02710.27641.0045-0.39060.9435-0.0222-0.00890.0239-0.00130.0121-0.05880.02020.0610.01580.0630.00590.00360.0792-0.00330.085924.717532.482425.19
52.52652.12150.41286.42382.74992.480.048-0.10930.0022-0.06890.0011-0.5956-0.14210.2369-0.02050.1039-0.0193-0.010.16710.03690.1529.75236.87148.8594
63.19490.6724-0.91495.0825-1.27453.9077-0.05170.0166-0.016-0.1897-0.2442-0.4910.04870.53730.25930.12630.0070.00510.19290.01830.122625.765926.9172-1.3716
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 41 )A3 - 41
2X-RAY DIFFRACTION2chain 'A' and (resid 42 through 93 )A42 - 93
3X-RAY DIFFRACTION3chain 'A' and (resid 94 through 175 )A94 - 175
4X-RAY DIFFRACTION4chain 'A' and (resid 176 through 293 )A176 - 293
5X-RAY DIFFRACTION5chain 'A' and (resid 294 through 317 )A294 - 317
6X-RAY DIFFRACTION6chain 'A' and (resid 318 through 345 )A318 - 345

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