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

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Basic information

Entry
Database: PDB / ID: 5lun
TitleEthylene Forming Enzyme from Pseudomonas syringae pv. phaseolicola - P1 ultra-high resolution crystal form in complex with iron, N-oxalylglycine and arginine
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
ARGININE / : / N-OXALYLGLYCINE / 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: 1.08 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
DepositionSep 9, 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 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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

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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)160,31919
Polymers158,5304
Non-polymers1,78915
Water36,9312050
1
A: 2-oxoglutarate-dependent ethylene/succinate-forming enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1035
Polymers39,6331
Non-polymers4704
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)40,1956
Polymers39,6331
Non-polymers5625
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)40,0114
Polymers39,6331
Non-polymers3783
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)40,0114
Polymers39,6331
Non-polymers3783
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.839, 79.056, 97.859
Angle α, β, γ (deg.)91.560, 93.420, 100.800
Int Tables number1
Space group name H-MP1

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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)


Mass: 39632.602 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas savastanoi pv. phaseolicola (bacteria)
Gene: efe / Plasmid: pColdI / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P32021, 2-oxoglutarate dioxygenase (ethene-forming), EC: 1.14.11.34

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Non-polymers , 5 types, 2065 molecules

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


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-OGA / N-OXALYLGLYCINE / N-Oxalylglycine


Mass: 147.086 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H5NO5 / Comment: inhibitor*YM
#4: Chemical
ChemComp-ARG / ARGININE / Arginine


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H15N4O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2050 / 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: 2.38 Å3/Da / Density % sol: 48.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% polyethylene glycol, 0.1 M Tris, 0.2 M sodium chloride, 0.01 M N-oxalylglycine, 0.02 M L-Arginine, protein concentration 15mg/mL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.08→77.6 Å / Num. obs: 584165 / % possible obs: 93 % / Redundancy: 3.5 % / Biso Wilson estimate: 11.557 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.053 / Net I/σ(I): 7.7
Reflection shellResolution: 1.08→1.12 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.822 / Mean I/σ(I) obs: 1.4 / CC1/2: 0.701 / % possible all: 89.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LSQ

5lsq


Resolution: 1.08→77.597 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 26.14
RfactorNum. reflection% reflection
Rfree0.1848 29143 5.04 %
Rwork0.162 --
obs0.1631 578420 92.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 75.14 Å2 / Biso mean: 21.1423 Å2 / Biso min: 6.3 Å2
Refinement stepCycle: final / Resolution: 1.08→77.597 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10721 0 204 2128 13053
Biso mean--21.78 31.81 -
Num. residues----1358
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01111501
X-RAY DIFFRACTIONf_angle_d1.39415663
X-RAY DIFFRACTIONf_chiral_restr0.081669
X-RAY DIFFRACTIONf_plane_restr0.0092070
X-RAY DIFFRACTIONf_dihedral_angle_d14.5594311
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.08-1.09230.41738560.4042168801773685
1.0923-1.10510.40758850.3886172181810386
1.1051-1.11860.39239520.3734171621811487
1.1186-1.13280.36919000.3618174251832587
1.1328-1.14770.37619230.3506174091833288
1.1477-1.16340.35039480.3384174911843988
1.1634-1.180.33449070.3191177761868389
1.18-1.19760.32069640.308177951875990
1.1976-1.21630.3239710.2959179541892590
1.2163-1.23630.30459270.284179071883490
1.2363-1.25760.29119430.2793180611900491
1.2576-1.28050.29089860.2701181231910991
1.2805-1.30510.28189490.2628180561900591
1.3051-1.33180.2789760.2451181861916292
1.3318-1.36070.25929330.2325184111934492
1.3607-1.39240.25229400.2116184551939593
1.3924-1.42720.233910230.1967184721949593
1.4272-1.46580.22310200.1808185921961293
1.4658-1.50890.19729720.1619185881956094
1.5089-1.55760.191910330.1475185791961293
1.5576-1.61330.167610710.1397186791975094
1.6133-1.67790.165210010.1354188091981095
1.6779-1.75430.16110090.1273189111992095
1.7543-1.84680.160510200.1256190622008296
1.8468-1.96250.14769380.1247189361987495
1.9625-2.1140.150410000.1248191242012496
2.114-2.32680.138410210.1186192102023197
2.3268-2.66350.143510490.1205192132026297
2.6635-3.35570.15169790.1299192792025897
3.3557-77.79820.139510470.1278195142056198

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