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- PDB-1zrr: Residual Dipolar Coupling Refinement of Acireductone Dioxygenase ... -

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Basic information

Entry
Database: PDB / ID: 1zrr
TitleResidual Dipolar Coupling Refinement of Acireductone Dioxygenase from Klebsiella
ComponentsE-2/E-2' protein
KeywordsOXIDOREDUCTASE / nickel / cupin / beta helix / methionine salvage
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
NICKEL (II) ION / Acireductone dioxygenase
Similarity search - Component
Biological speciesKlebsiella oxytoca (bacteria)
MethodSOLUTION NMR / combined torsional, cartesian dynamics simulated annealing with residual dipolar couplings, NOE, chemical shift, dihedral restraints
AuthorsPochapsky, T.C. / Pochapsky, S.S. / Ju, T. / Hoefler, C. / Liang, J.
Citation
Journal: J.Biomol.NMR / Year: 2006
Title: A refined model for the structure of acireductone dioxygenase from Klebsiella ATCC 8724 incorporating residual dipolar couplings
Authors: Pochapsky, T.C. / Pochapsky, S.S. / Ju, T. / Hoefler, C. / Liang, J.
#1: Journal: Nat.Struct.Biol. / Year: 2002
Title: Modeling and experiment yields the structure of acireductone dioxygenase from Klebsiella pneumoniae
Authors: Pochapsky, T.C. / Pochapsky, S.S. / Ju, T. / Mo, H. / Al-Mjeni, F. / Maroney, M.J.
#2: Journal: Biochemistry / Year: 2001
Title: Mechanistic Studies of two Dioxygenases from the methionine salvage pathway of Klebsiella pneumoniae
Authors: Dai, Y. / Pochapsky, T.C. / Abeles, R.H.
History
DepositionMay 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2005Provider: repository / Type: Initial release
SupersessionOct 24, 2006ID: 1M4O
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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 22, 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)20,2782
Polymers20,2191
Non-polymers591
Water362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)17 / -
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) / Plasmid: pET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9ZFE7
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


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

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Sample preparation

DetailsContents: 1 mM aRD 15N labeled in 5% orienting medium (either filamentous phage or C12E5 polymer) pH 7.4, 20 mM KPi; 90/10 H2O/D2O
Solvent system: 90/10 H2O/D2O

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NMR measurement

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

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Processing

NMR softwareName: X-PLOR / Version: 2.1 / Classification: refinement
RefinementMethod: combined torsional, cartesian dynamics simulated annealing with residual dipolar couplings, NOE, chemical shift, dihedral restraints
Software ordinal: 1
Details: Metal binding site modeled from XAFS data, paramagnetically broadened backbone residues modeled from pdb entry 1VR3 (ARD homologue from Mus musculus).
NMR representativeSelection criteria: closest to the average
NMR ensembleConformers submitted total number: 17

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