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- PDB-2hji: Structural model for the Fe-containing isoform of acireductone di... -

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Basic information

Entry
Database: PDB / ID: 2hji
TitleStructural model for the Fe-containing isoform of acireductone dioxygenase
ComponentsE-2/E-2' protein
KeywordsOXIDOREDUCTASE / dioxygenase / non-heme iron / isozyme / methionine salvage / structural entropy
Function / homology
Function and homology information


acireductone dioxygenase (Ni2+-requiring) / acireductone dioxygenase [iron(II)-requiring] / acireductone dioxygenase (Ni2+-requiring) activity / acireductone dioxygenase [iron(II)-requiring] activity / L-methionine salvage from S-adenosylmethionine / L-methionine salvage from methylthioadenosine / nickel cation binding / iron ion binding
Similarity search - Function
Acireductone dioxygenase ARD, bacteria / Acireductone dioxygenase ARD family / ARD/ARD' family / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Acireductone dioxygenase
Similarity search - Component
Biological speciesKlebsiella oxytoca (bacteria)
MethodSOLUTION NMR / restrained simulated annealing using torsional dynamics
AuthorsPochapsky, T.C. / Ju, T. / Maroney, M.J. / Chai, S.C.
Citation
Journal: J.Mol.Biol. / Year: 2006
Title: One Protein, Two Enzymes Revisited: A Structural Entropy Switch Interconverts the Two Isoforms of Acireductone Dioxygenase
Authors: Ju, T. / Goldsmith, R.B. / Chai, S.C. / Maroney, M.J. / Pochapsky, S.S. / Pochapsky, T.C.
#1: Journal: J.Biol.Chem. / Year: 1999
Title: One protein, two enzymes.
Authors: Dai, Y. / Wensink, P. / Abeles, R.A.
History
DepositionJun 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site
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.ptnr1_label_seq_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E-2/E-2' protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2752
Polymers20,2191
Non-polymers561
Water362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)14 / 300back calculated data agree with experimental NOESY spectrum,structures with acceptable covalent geometry
RepresentativeModel #1closest to the average

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Components

#1: Protein E-2/E-2' protein


Mass: 20219.412 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella oxytoca (bacteria) / Strain: ATCC 8724 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: Q9ZFE7, acireductone dioxygenase [iron(II)-requiring]
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
131HNHA
NMR detailsText: residual dipolar couplings obtained using filamentous phage (fd) and C12E5 polyol

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Sample preparation

DetailsContents: uniform 15N, 13C labeled, 1 mM / Solvent system: 90/10 H2O/D2O 50 mM KPi buffer, pH 7.5
Sample conditionsIonic strength: 50 mM KPi / pH: 7.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 600 MHz

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Processing

NMR softwareName: CNS / Developer: Brunger A. T. etall / Classification: refinement
RefinementMethod: restrained simulated annealing using torsional dynamics
Software ordinal: 1
Details: Only residues 1-156 are included in structural models, as residues 157-179 are disordered in solution.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum,structures with acceptable covalent geometry
Conformers calculated total number: 300 / Conformers submitted total number: 14

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