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- PDB-6cba: Ethylene forming enzyme in complex with manganese, 2-oxoglutarate... -

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Basic information

Entry
Database: PDB / ID: 6cba
TitleEthylene forming enzyme in complex with manganese, 2-oxoglutarate and canavanine
Components2-oxoglutarate-dependent ethylene/succinate-forming enzyme
KeywordsOXIDOREDUCTASE / manganese / 2-oxoglutarate / canavanine
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 / L-CANAVANINE / : / 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: 1.13 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: 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
DepositionFeb 2, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.type / _database_2.pdbx_DOI ..._chem_comp.type / _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
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2
Revision 2.1Apr 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

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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)40,0944
Polymers39,7171
Non-polymers3773
Water8,467470
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.430, 81.570, 87.630
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.: 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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GGB / L-CANAVANINE / L-2-AMINO-4-(GUANIDINOOXY)BUTYRIC ACID


Type: L-peptide linking / Mass: 176.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12N4O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 470 / 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: 2.18 Å3/Da / Density % sol: 43.55 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.5 ul 64 mg/ml EFE (1 mM manganese chloride, 25 mM HEPES pH 8.0, 1 mM TCEP, 3 mM canavanine, 2 mM 2-oxoglutarate) was mixed with 0.5 ul reservoir solution. The sitting drop reservoir of 200 ...Details: 0.5 ul 64 mg/ml EFE (1 mM manganese chloride, 25 mM HEPES pH 8.0, 1 mM TCEP, 3 mM canavanine, 2 mM 2-oxoglutarate) was mixed with 0.5 ul reservoir solution. The sitting drop reservoir of 200 ul contained 25% w/v Polyethylene glycol 3,350, 0.1 M Bis-Tris pH 6.5, 0.2 M sodium chloride. 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: 0.9762 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.13→48.43 Å / Num. obs: 128283 / % possible obs: 98.5 % / Redundancy: 7.2 % / Biso Wilson estimate: 9.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.032 / Rrim(I) all: 0.087 / Net I/σ(I): 11.3 / Num. measured all: 924312 / Scaling rejects: 1146
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.13-1.156.50.86262210.8040.3620.93897.5
6.19-48.436.90.0379140.9990.0150.0499.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.98 Å42.39 Å
Translation5.98 Å42.39 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.5.32data scaling
PHASER2.7.16phasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5V2Z

5v2z


Resolution: 1.13→32.491 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 16.24
RfactorNum. reflection% reflection
Rfree0.1629 11971 4.86 %
Rwork0.1415 --
obs0.1426 123240 98.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 58.74 Å2 / Biso mean: 16.374 Å2 / Biso min: 5.69 Å2
Refinement stepCycle: final / Resolution: 1.13→32.491 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2750 0 38 470 3258
Biso mean--16.89 27.52 -
Num. residues----347
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 (%)
1.13-1.14280.26993740.25147660803496
1.1428-1.15630.24624300.23297748817898
1.1563-1.17040.25263740.22587786816098
1.1704-1.18520.23184420.22247943838599
1.1852-1.20080.23073810.21587841822299
1.2008-1.21730.22143800.2047874825499
1.2173-1.23460.21184180.20187839825798
1.2346-1.25310.20853860.19117843822999
1.2531-1.27270.2213730.19497908828198
1.2727-1.29350.23084040.18517751815598
1.2935-1.31580.19053970.17477896829398
1.3158-1.33980.1923410.16467799814098
1.3398-1.36550.18834220.16237708813098
1.3655-1.39340.1944220.1587853827598
1.3934-1.42370.18854200.15427678809897
1.4237-1.45680.16353990.1457528792795
1.4568-1.49320.13734120.12497907831999
1.4932-1.53360.14184130.1237873828699
1.5336-1.57870.15724530.12327886833999
1.5787-1.62970.1483840.11697892827699
1.6297-1.68790.14023910.12157892828399
1.6879-1.75550.14173960.11867900829699
1.7555-1.83540.14363890.11827844823399
1.8354-1.93220.13044390.11287852829199
1.9322-2.05320.14084290.11927749817898
2.0532-2.21170.13783790.11897835821498
2.2117-2.43420.14823510.1227594794595
2.4342-2.78630.15623730.1297685805897
2.7863-3.50970.15384050.134879898394100
3.5097-32.50460.15423940.13979568350100

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