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- PDB-5v2v: Ethylene forming enzyme in complex with nickel -

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Basic information

Entry
Database: PDB / ID: 5v2v
TitleEthylene forming enzyme in complex with nickel
Components2-oxoglutarate-dependent ethylene/succinate-forming enzyme
KeywordsOXIDOREDUCTASE / 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
NICKEL (II) ION / 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: 3.04 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 / Category: diffrn_detector / pdbx_audit_support
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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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 / _struct_conn.ptnr2_label_seq_id
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)40,1982
Polymers40,1391
Non-polymers591
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.790, 79.310, 87.750
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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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: 40138.809 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-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.81 Å3/Da / Density % sol: 32.1 % / Mosaicity: 1.57 °
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.5 ul 72 mg/ml EFE (25 mM HEPES pH 8.0, 1 mM TCEP) was mixed with 0.5 ul reservoir solution. The sitting drop reservoir of 200 ul contained 0.2 M lithium chloride, 0.1 M Tris-HCl pH 8.0, ...Details: 0.5 ul 72 mg/ml EFE (25 mM HEPES pH 8.0, 1 mM TCEP) was mixed with 0.5 ul reservoir solution. The sitting drop reservoir of 200 ul contained 0.2 M lithium chloride, 0.1 M Tris-HCl pH 8.0, 20% w/v Polyethylene glycol 6,000. A grown crystal was soaked for 2 hours in a sitting drop containing 0.1 M nickel chloride, 0.2 M lithium chloride, 0.1 M Tris-HCl pH 8.0, 20% w/v Polyethylene glycol 6,000, the reservoir of 100 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 direcly frozen.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.4777 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4777 Å / Relative weight: 1
ReflectionResolution: 3.04→87.75 Å / Num. obs: 5959 / % possible obs: 99.3 % / Redundancy: 4.8 % / Biso Wilson estimate: 54.66 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.069 / Rrim(I) all: 0.157 / Net I/σ(I): 7 / Num. measured all: 28385 / Scaling rejects: 32
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) all% possible all
3.04-3.225.10.3829410.9410.1810.42499.7
9.12-87.754.60.0690.990.0360.07899.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.24 Å43.88 Å
Translation5.24 Å43.88 Å

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Processing

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

5v2t


Resolution: 3.04→43.875 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 28.96
RfactorNum. reflection% reflection
Rfree0.2675 847 14.37 %
Rwork0.1988 --
obs0.2086 5308 97.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 108.48 Å2 / Biso mean: 47.67 Å2 / Biso min: 23.31 Å2
Refinement stepCycle: final / Resolution: 3.04→43.875 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2316 0 1 2 2319
Biso mean--52.01 44.13 -
Num. residues----300
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052390
X-RAY DIFFRACTIONf_angle_d0.5333247
X-RAY DIFFRACTIONf_chiral_restr0.039349
X-RAY DIFFRACTIONf_plane_restr0.005422
X-RAY DIFFRACTIONf_dihedral_angle_d2.6651393
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0401-3.13820.35491420.290281896099
3.1382-3.25040.33751280.264684897699
3.2504-3.38050.2891360.230684798398
3.3805-3.53430.30281600.199880296299
3.5343-3.72050.24741350.215484798298
3.7205-3.95350.27991150.191184295799
3.9535-4.25850.23971600.164782198198
4.2585-4.68660.24281550.173681196697
4.6866-5.36370.27381360.167977791393
5.3637-6.75370.22991160.195383795397
6.7537-43.87950.2551430.199784098399

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