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- PDB-5v34: Ethylene forming enzyme in complex with manganese, malic acid and... -

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Basic information

Entry
Database: PDB / ID: 5v34
TitleEthylene forming enzyme in complex with manganese, malic acid and L-arginine
Components2-oxoglutarate-dependent ethylene/succinate-forming enzyme
KeywordsOXIDOREDUCTASE / ethylene biosynthesis
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 / D-MALATE / : / 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: 1.48 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 / Data collection / Refinement description
Category: diffrn_detector / pdbx_audit_support / software
Item: _diffrn_detector.detector / _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_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_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.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)40,0814
Polymers39,7171
Non-polymers3643
Water8,521473
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.360, 87.360, 104.300
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-543-

HOH

21A-799-

HOH

31A-956-

HOH

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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-ARG / ARGININE / Arginine


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID / Malic acid


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 473 / 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: 2.89 Å3/Da / Density % sol: 57.48 % / Mosaicity: 0.38 °
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 ul 64 mg/ml EFE (+1 mM manganese chloride, 25 mM HEPES pH 8.0, 1 mM TCEP, +2.5 mM L-arginine) was mixed with 0.2 ul reservoir solution. The sitting drop reservoir of 50 ul contained 25% ...Details: 0.2 ul 64 mg/ml EFE (+1 mM manganese chloride, 25 mM HEPES pH 8.0, 1 mM TCEP, +2.5 mM L-arginine) was mixed with 0.2 ul reservoir solution. The sitting drop reservoir of 50 ul contained 25% PEG 1500 and 0.1 M MMT buffer, pH 6.5. 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-D / Wavelength: 1.1272 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1272 Å / Relative weight: 1
ReflectionResolution: 1.48→61.24 Å / Num. obs: 75179 / % possible obs: 97.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 16.94 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.033 / Rrim(I) all: 0.091 / Net I/σ(I): 12.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) all% possible all
1.48-1.517.41.05436050.6390.4091.13396.4
8.11-61.246.80.0670.9910.0270.07399.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.2 Å61.24 Å
Translation6.2 Å61.24 Å

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.5.31data scaling
PHASER2.7.16phasing
PHENIX1.11.1-2575refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5V2T

5v2t


Resolution: 1.48→43.68 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 15.51
RfactorNum. reflection% reflection
Rfree0.1621 7113 4.92 %
Rwork0.1352 --
obs0.1365 72267 97.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 73.51 Å2 / Biso mean: 23.777 Å2 / Biso min: 10.86 Å2
Refinement stepCycle: final / Resolution: 1.48→43.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2721 0 41 473 3235
Biso mean--19.71 34.02 -
Num. residues----342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012883
X-RAY DIFFRACTIONf_angle_d1.0293914
X-RAY DIFFRACTIONf_chiral_restr0.078416
X-RAY DIFFRACTIONf_plane_restr0.008517
X-RAY DIFFRACTIONf_dihedral_angle_d14.851064
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 (%)
1.48-1.49680.32662780.28144376465495
1.4968-1.51440.36392400.27874475471596
1.5144-1.53290.26222550.26484569482496
1.5329-1.55230.23361970.23054529472697
1.5523-1.57270.24982330.21584634486797
1.5727-1.59430.21652410.20824557479897
1.5943-1.61710.27032420.19754597483997
1.6171-1.64120.21332690.17964546481597
1.6412-1.66680.20652070.16374538474597
1.6668-1.69420.1762020.15384632483497
1.6942-1.72340.19652180.15454622484098
1.7234-1.75470.19242380.14524607484598
1.7547-1.78850.17672960.14814587488398
1.7885-1.8250.19882300.13864589481998
1.825-1.86470.16092500.14014623487398
1.8647-1.9080.16912110.13164090430188
1.908-1.95580.14822420.12474579482198
1.9558-2.00860.15722360.11594652488899
2.0086-2.06770.15012430.11464645488899
2.0677-2.13450.13782600.11434674493499
2.1345-2.21080.14362600.11124595485599
2.2108-2.29930.13932440.10814706495099
2.2993-2.40390.15282700.10744585485599
2.4039-2.53060.14111920.10844702489499
2.5306-2.68920.1552180.11094740495899
2.6892-2.89680.15592230.11784702492599
2.8968-3.18820.14613060.129446094915100
3.1882-3.64930.14541930.13464184437788
3.6493-4.5970.13022310.122847424973100
4.597-43.69890.16341880.152547354923100

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