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- PDB-4emj: Complex between the reductase and ferredoxin components of toluen... -

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Basic information

Entry
Database: PDB / ID: 4emj
TitleComplex between the reductase and ferredoxin components of toluene dioxygenase
Components
  • TodA
  • Toluene 1,2-dioxygenase system ferredoxin subunit
KeywordsOXIDOREDUCTASE / Oxidoreductase complex / toluene dioxygenase oxygenase component
Function / homology
Function and homology information


ferredoxin-NAD+ reductase / ferredoxin-NAD+ reductase activity / toluene catabolic process / oxidoreductase activity, acting on NAD(P)H / dioxygenase activity / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / metal ion binding / cytoplasm
Similarity search - Function
Reductase, C-terminal / Reductase C-terminal / : / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / FAD/NAD-linked reductase, C-terminal dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain ...Reductase, C-terminal / Reductase C-terminal / : / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / FAD/NAD-linked reductase, C-terminal dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / Toluene 1,2-dioxygenase system ferredoxin--NAD(+) reductase component / Toluene 1,2-dioxygenase system ferredoxin subunit / Toluene 1,2-dioxygenase system ferredoxin subunit / Ferredoxin reductase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLin, T.Y. / Werther, T. / Jeoung, J.H. / Dobbek, H.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Suppression of Electron Transfer to Dioxygen by Charge Transfer and Electron Transfer Complexes in the FAD-dependent Reductase Component of Toluene Dioxygenase.
Authors: Lin, T.Y. / Werther, T. / Jeoung, J.H. / Dobbek, H.
History
DepositionApr 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TodA
B: Toluene 1,2-dioxygenase system ferredoxin subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8484
Polymers54,8862
Non-polymers9612
Water4,378243
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.290, 120.290, 60.420
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein TodA / Toluene dioxygenase reductase TobA / Toluene dioxygenase reductase component


Mass: 42983.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: F1 / Gene: tobA, todA / Production host: Escherichia coli (E. coli) / References: UniProt: Q7BPB6, UniProt: A5W4E9*PLUS
#2: Protein Toluene 1,2-dioxygenase system ferredoxin subunit


Mass: 11902.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: F1 / Gene: todB / Production host: Escherichia coli (E. coli) / References: UniProt: P0C620, UniProt: A5W4F0*PLUS
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% (w/v) polyethylene glycol monomethyl ether 5,000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jan 11, 2011
RadiationMonochromator: Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.4→33 Å / Num. all: 19663 / Num. obs: 19644 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.2_432)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→30.07 Å / SU ML: 0.7 / σ(F): 1.4 / Phase error: 20.64 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.234 982 5 %
Rwork0.169 --
obs0.172 19637 99.9 %
all-19644 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.7 Å2 / ksol: 0.33 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.1122 Å2-0 Å20 Å2
2---0.1122 Å2-0 Å2
3---0.2244 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3808 0 57 243 4108
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153989
X-RAY DIFFRACTIONf_angle_d1.665435
X-RAY DIFFRACTIONf_dihedral_angle_d15.5611441
X-RAY DIFFRACTIONf_chiral_restr0.137622
X-RAY DIFFRACTIONf_plane_restr0.007712
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.52660.30731390.22662633X-RAY DIFFRACTION100
2.5266-2.68480.251390.19122646X-RAY DIFFRACTION100
2.6848-2.89190.24471410.18432667X-RAY DIFFRACTION100
2.8919-3.18270.27431390.1732653X-RAY DIFFRACTION100
3.1827-3.64250.23151410.16322666X-RAY DIFFRACTION100
3.6425-4.58660.17851400.13412669X-RAY DIFFRACTION100
4.5866-30.07480.22651430.16292721X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 39.9004 Å / Origin y: 9.8319 Å / Origin z: -4.9915 Å
111213212223313233
T0.0645 Å2-0.036 Å2-0.0067 Å2-0.1496 Å2-0.0031 Å2--0.2034 Å2
L0.6206 °2-0.4446 °2-0.334 °2-0.8152 °20.2755 °2--1.3473 °2
S0.0119 Å °-0.0916 Å °0.1831 Å °0.0083 Å °0.0539 Å °-0.2941 Å °-0.1007 Å °0.2777 Å °0.0494 Å °
Refinement TLS groupSelection details: all

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