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- PDB-5v2x: Ethylene forming enzyme in complex with manganese and 2-oxoglutarate -

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Basic information

Entry
Database: PDB / ID: 5v2x
TitleEthylene forming enzyme in complex with manganese and 2-oxoglutarate
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 / : / 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: 1.847 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 ...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_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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)80,1288
Polymers79,4342
Non-polymers6946
Water17,799988
1
A: 2-oxoglutarate-dependent ethylene/succinate-forming enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0644
Polymers39,7171
Non-polymers3473
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 2-oxoglutarate-dependent ethylene/succinate-forming enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0644
Polymers39,7171
Non-polymers3473
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.411, 97.546, 102.385
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.: 2 / Mutation: 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: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H6O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 988 / 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: 47.41 % / Mosaicity: 0.12 °
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.18 ul 61 mg/ml EFE (25 mM HEPES pH 8.0, 1 mM TCEP, 0.6 mM 2-oxoglutarate) was mixed with 0.18 ul reservoir solution. The sitting drop reservoir of 50 ul contained 0.2 M lithium chloride, 0. ...Details: 0.18 ul 61 mg/ml EFE (25 mM HEPES pH 8.0, 1 mM TCEP, 0.6 mM 2-oxoglutarate) was mixed with 0.18 ul reservoir solution. The sitting drop reservoir of 50 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 soaked for about a minute in 25% glycerol, 75% reservoir solution before freezing it.

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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: Oct 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.847→45.33 Å / Num. obs: 64351 / % possible obs: 99.6 % / Redundancy: 5.8 % / Biso Wilson estimate: 13.49 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.06 / Rrim(I) all: 0.145 / Net I/σ(I): 11.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) all% possible all
1.847-1.895.60.74437890.830.3410.8295.9
9.05-45.334.80.030.9990.0150.03398.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.12 Å44.03 Å
Translation5.12 Å44.03 Å

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Processing

Software
NameVersionClassification
Aimless0.5.28data 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: 1.847→44.032 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 20.6
RfactorNum. reflection% reflection
Rfree0.2008 3316 5.18 %
Rwork0.1625 --
obs0.1645 61427 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 65.42 Å2 / Biso mean: 18.126 Å2 / Biso min: 5.45 Å2
Refinement stepCycle: final / Resolution: 1.847→44.032 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5472 0 42 994 6508
Biso mean--18.2 29.97 -
Num. residues----690
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075717
X-RAY DIFFRACTIONf_angle_d0.757754
X-RAY DIFFRACTIONf_chiral_restr0.049821
X-RAY DIFFRACTIONf_plane_restr0.0061022
X-RAY DIFFRACTIONf_dihedral_angle_d3.0484702
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 (%)
1.8473-1.86830.26351600.25873571373191
1.8683-1.89030.29062040.234639394143100
1.8903-1.91340.30111890.239639284117100
1.9134-1.93760.22691900.23339034093100
1.9376-1.96310.28561880.225939014089100
1.9631-1.990.24032110.214939124123100
1.99-2.01840.24792510.21238554106100
2.0184-2.04850.22952170.203839014118100
2.0485-2.08050.23751780.192839624140100
2.0805-2.11470.23952190.183938744093100
2.1147-2.15110.21962190.176138804099100
2.1511-2.19020.23152390.181438644103100
2.1902-2.23240.18052320.167138504082100
2.2324-2.27790.20492500.17138944144100
2.2779-2.32740.21462360.165338364072100
2.3274-2.38160.19882190.157938944113100
2.3816-2.44110.21861760.15139294105100
2.4411-2.50710.20312330.15238934126100
2.5071-2.58090.1842160.147638984114100
2.5809-2.66420.22891990.152238964095100
2.6642-2.75940.18992320.148838604092100
2.7594-2.86990.19971900.145439574147100
2.8699-3.00050.2022030.153938514054100
3.0005-3.15860.20271860.151939554141100
3.1586-3.35640.18182680.145738384106100
3.3564-3.61550.15892330.13138954128100
3.6155-3.97910.15812310.125438524083100
3.9791-4.55440.14512100.114239244134100
4.5544-5.7360.16741800.140239104090100
5.736-44.04470.21752050.17743869407499

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