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- PDB-3ef6: Crystal structure of Toluene 2,3-Dioxygenase Reductase -

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Basic information

Entry
Database: PDB / ID: 3ef6
TitleCrystal structure of Toluene 2,3-Dioxygenase Reductase
ComponentsToluene 1,2-dioxygenase system ferredoxin--NAD(+) reductase
KeywordsOXIDOREDUCTASE / FAD binding protein / NADH binding protein / Aromatic hydrocarbons catabolism / FAD / Flavoprotein / NAD
Function / homology
Function and homology information


ferredoxin-NAD+ reductase / ferredoxin-NAD+ reductase activity / toluene catabolic process / oxidoreductase activity, acting on NAD(P)H / cytoplasm
Similarity search - Function
Reductase, C-terminal / Reductase C-terminal / : / FAD/NAD-linked reductase, C-terminal dimerisation domain / FAD/NAD-linked reductase, dimerisation 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 ...Reductase, C-terminal / Reductase C-terminal / : / FAD/NAD-linked reductase, C-terminal dimerisation domain / FAD/NAD-linked reductase, dimerisation 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 / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Toluene 1,2-dioxygenase system ferredoxin--NAD(+) reductase component
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsFriemann, R. / Lee, K. / Brown, E.N. / Gibson, D.T. / Eklund, H. / Ramaswamy, S.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Structures of the multicomponent Rieske non-heme iron toluene 2,3-dioxygenase enzyme system
Authors: Friemann, R. / Lee, K. / Brown, E.N. / Gibson, D.T. / Eklund, H. / Ramaswamy, S.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2005
Title: Purification, crystallization and preliminary X-ray diffraction studies of the three components of the toluene 2,3-dioxygenase enzyme system
Authors: Lee, K. / Friemann, R. / Parales, J.V. / Gibson, D.T. / Ramaswamy, S.
History
DepositionSep 8, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Toluene 1,2-dioxygenase system ferredoxin--NAD(+) reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,60611
Polymers42,9841
Non-polymers1,62210
Water8,377465
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.128, 77.128, 156.372
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-4135-

HOH

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Components

#1: Protein Toluene 1,2-dioxygenase system ferredoxin--NAD(+) reductase


Mass: 42983.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Escherichia coli CGSC#7692 (pDTG601A) contain the cloned todC1C2BA genes that encode the Oxygenase, Ferredoxin and Reductase parts of the Toluene 2,3-Dioxygenase System
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: F1 / Gene: Pput_2878, todA, todC1C2BA / Plasmid: pDTG601A / Production host: Escherichia coli (E. coli) / Strain (production host): CGSC#7692 / References: UniProt: A5W4E9, ferredoxin-NAD+ reductase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 465 / 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: 2.71 Å3/Da / Density % sol: 54.53 %
Crystal growTemperature: 286 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: 0.1 M Tris pH 8.5, 1.5 M (NH)4SO 2 and 12% (v/v) glycerol, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 286K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.0332 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 21, 2004
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.8→19.86 Å / Num. obs: 44352 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 9.24 % / Rmerge(I) obs: 0.076 / Χ2: 0.92 / Scaling rejects: 3098
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 7.04 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 4 / Num. measured all: 29700 / Num. unique all: 4216 / Χ2: 1.08 / % possible all: 96.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.583 / Cor.coef. Fo:Fc: 0.206
Highest resolutionLowest resolution
Rotation3 Å31.6 Å
Translation3 Å31.6 Å

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Processing

Software
NameVersionClassificationNB
d*TREK9.1Ldata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry: 1D7Y including all side chains

1d7y


Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.841 / SU B: 2.762 / SU ML: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.243 2229 5 %RANDOM
Rwork0.203 ---
all0.205 44198 --
obs0.205 44198 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 69.91 Å2 / Biso mean: 28.002 Å2 / Biso min: 11.65 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å20 Å20 Å2
2--1.09 Å20 Å2
3----2.18 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2940 0 105 465 3510
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0213154
X-RAY DIFFRACTIONr_angle_refined_deg1.5212.0054293
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6225415
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.3122.683123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.77915492
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7761534
X-RAY DIFFRACTIONr_chiral_restr0.0910.2493
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022361
X-RAY DIFFRACTIONr_nbd_refined0.1950.21524
X-RAY DIFFRACTIONr_nbtor_refined0.2970.22136
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2436
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.220.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.213
X-RAY DIFFRACTIONr_mcbond_it0.861.52066
X-RAY DIFFRACTIONr_mcangle_it1.29923218
X-RAY DIFFRACTIONr_scbond_it2.07131291
X-RAY DIFFRACTIONr_scangle_it3.3894.51075
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 140 -
Rwork0.254 3026 -
all-3166 -
obs--98.81 %

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