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- PDB-8uc2: Ethylene forming enzyme (EFE) R171A variant in complex with nicke... -

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Basic information

Entry
Database: PDB / ID: 8uc2
TitleEthylene forming enzyme (EFE) R171A variant in complex with nickel and Benzoic acid
Components2-oxoglutarate-dependent ethylene/succinate-forming enzyme
KeywordsOXIDOREDUCTASE
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 / 2-oxoglutarate-dependent 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
BENZOIC ACID / 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 / Resolution: 1.6 Å
AuthorsChatterjee, S. / Rankin, J.A. / Hu, J. / Hausinger, R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE2203472 United States
National Science Foundation (NSF, United States)CHE1904295 United States
CitationJournal: Biochemistry / Year: 2024
Title: Structural, Spectroscopic, and Computational Insights from Canavanine-Bound and Two Catalytically Compromised Variants of the Ethylene-Forming Enzyme.
Authors: Chatterjee, S. / Fellner, M. / Rankin, J. / Thomas, M.G. / J S Rifayee, S.B. / Christov, C.Z. / Hu, J. / Hausinger, R.P.
History
DepositionSep 25, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 1, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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)39,7506
Polymers39,4051
Non-polymers3455
Water8,359464
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.109, 97.490, 98.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 2-oxoglutarate-dependent ethylene/succinate-forming enzyme


Mass: 39405.426 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(DE3) (bacteria) / References: UniProt: P32021

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Non-polymers , 5 types, 469 molecules

#2: Chemical ChemComp-BEZ / BENZOIC ACID / Benzoic acid


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 464 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.49 Å3/Da / Density % sol: 50.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium citrate tribasic dihydrate, 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.6→62.03 Å / Num. obs: 47283 / % possible obs: 93 % / Redundancy: 5.8 % / CC1/2: 0.999 / Net I/σ(I): 20
Reflection shellResolution: 1.6→1.63 Å / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1380 / CC1/2: 0.906

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Processing

Software
NameVersionClassification
PHENIX(1.19_4092: ???)refinement
HKL-2000data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→62.03 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 19.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1864 2358 4.99 %
Rwork0.1693 --
obs0.1701 47228 92.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→62.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2659 0 19 464 3142
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072845
X-RAY DIFFRACTIONf_angle_d0.9143870
X-RAY DIFFRACTIONf_dihedral_angle_d14.9581041
X-RAY DIFFRACTIONf_chiral_restr0.059409
X-RAY DIFFRACTIONf_plane_restr0.01511
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.630.3013690.29051583X-RAY DIFFRACTION56
1.63-1.670.28151100.25081855X-RAY DIFFRACTION66
1.67-1.710.25361070.21582151X-RAY DIFFRACTION77
1.71-1.750.24651230.19722458X-RAY DIFFRACTION88
1.75-1.80.21091250.18832638X-RAY DIFFRACTION93
1.8-1.850.19021450.1822753X-RAY DIFFRACTION98
1.85-1.910.21771680.18972783X-RAY DIFFRACTION100
1.91-1.980.17621510.18972836X-RAY DIFFRACTION100
1.98-2.060.17911380.16692827X-RAY DIFFRACTION100
2.06-2.150.22691410.16762833X-RAY DIFFRACTION100
2.15-2.260.17781670.16582818X-RAY DIFFRACTION100
2.26-2.410.21760.16632811X-RAY DIFFRACTION100
2.41-2.590.18141520.16192843X-RAY DIFFRACTION100
2.59-2.850.16541350.17342890X-RAY DIFFRACTION100
2.85-3.270.17671590.17132853X-RAY DIFFRACTION100
3.27-4.110.15961370.14522910X-RAY DIFFRACTION100
4.11-62.030.18271550.16133028X-RAY DIFFRACTION100
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)
13.8425-0.6607-0.32866.80373.92547.58790.03030.179-0.11260.02970.2435-0.521-0.1090.3831-0.27380.17580.023600.1455-0.01370.226725.5941-1.377122.2176
21.03990.2326-0.87791.9455-0.6361.9557-0.0421-0.01980.01240.13190.03970.1326-0.0835-0.05880.00990.0559-0.0091-0.02750.1023-0.03070.111113.499918.42118.256
31.03030.3197-0.57961.620.54732.1767-0.04820.02180.0015-0.01670.03-0.0386-0.00970.09590.0220.06730.0082-0.02370.08280.01080.088721.000322.266914.6157
42.46510.21911.07623.2044-1.17990.98030.04850.2019-0.1177-0.35540.016-0.41630.11960.6444-0.06920.18680.00370.0520.1925-0.02840.247129.43888.578711.5139
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 318 through 345 )
2X-RAY DIFFRACTION2chain 'A' and (resid 3 through 123 )
3X-RAY DIFFRACTION3chain 'A' and (resid 124 through 293 )
4X-RAY DIFFRACTION4chain 'A' and (resid 294 through 317 )

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