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- PDB-3eqq: Apo Toluene 2,3-Dioxygenase -

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Basic information

Entry
Database: PDB / ID: 3eqq
TitleApo Toluene 2,3-Dioxygenase
Components
  • Benzene 1,2-dioxygenase subunit alpha
  • Benzene 1,2-dioxygenase subunit beta
KeywordsOXIDOREDUCTASE / Rieske iron sulfur binding protein / apo-structure / 2Fe-2S / Aromatic hydrocarbons catabolism / Dioxygenase / Iron / Iron-sulfur / Metal-binding / NAD
Function / homology
Function and homology information


toluene dioxygenase / benzene 1,2-dioxygenase / benzene 1,2-dioxygenase activity / toluene dioxygenase activity / xylene catabolic process / toluene catabolic process / 2 iron, 2 sulfur cluster binding / iron ion binding
Similarity search - Function
Ring-hydroxylating dioxygenase, alpha subunit NdoB-like, C-terminal / Ring hydroxylating beta subunit / Ring-hydroxylating dioxygenase beta subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit, C-terminal domain / Ring hydroxylating alpha subunit (catalytic domain) / Aromatic-ring-hydroxylating dioxygenase, 2Fe-2S-binding site / Bacterial ring hydroxylating dioxygenases alpha-subunit signature. / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 ...Ring-hydroxylating dioxygenase, alpha subunit NdoB-like, C-terminal / Ring hydroxylating beta subunit / Ring-hydroxylating dioxygenase beta subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit, C-terminal domain / Ring hydroxylating alpha subunit (catalytic domain) / Aromatic-ring-hydroxylating dioxygenase, 2Fe-2S-binding site / Bacterial ring hydroxylating dioxygenases alpha-subunit signature. / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / Nuclear Transport Factor 2; Chain: A, - #50 / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / FE2/S2 (INORGANIC) CLUSTER / Benzene 1,2-dioxygenase subunit beta / Benzene 1,2-dioxygenase subunit alpha / Benzene 1,2-dioxygenase subunit alpha / Benzene 1,2-dioxygenase subunit beta
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 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
DepositionOct 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: Benzene 1,2-dioxygenase subunit alpha
B: Benzene 1,2-dioxygenase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,2784
Polymers73,0462
Non-polymers2322
Water0
1
A: Benzene 1,2-dioxygenase subunit alpha
B: Benzene 1,2-dioxygenase subunit beta
hetero molecules

A: Benzene 1,2-dioxygenase subunit alpha
B: Benzene 1,2-dioxygenase subunit beta
hetero molecules

A: Benzene 1,2-dioxygenase subunit alpha
B: Benzene 1,2-dioxygenase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,83312
Polymers219,1386
Non-polymers6956
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_656-z+1,x+1/2,-y+3/21
crystal symmetry operation11_466y-1/2,-z+3/2,-x+11
Buried area32400 Å2
ΔGint-56 kcal/mol
Surface area56670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)235.873, 235.873, 235.873
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332
Components on special symmetry positions
IDModelComponents
11B-188-

FE2

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Components

#1: Protein Benzene 1,2-dioxygenase subunit alpha / / Benzene 1 / 2-dioxygenase P1 subunit / Toluene 2 / 3-dioxygenase subunit alpha


Mass: 51004.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: F1 / Gene: bnzA, todC1 / Production host: Escherichia coli (E. coli) / Strain (production host): CGSC#7692
References: UniProt: P0C618, UniProt: A5W4F2*PLUS, toluene dioxygenase
#2: Protein Benzene 1,2-dioxygenase subunit beta / / Benzene 1 / 2-dioxygenase P2 subunit / Toluene 2 / 3-dioxygenase subunit beta


Mass: 22041.807 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: F1 / Gene: bnzB, todC2 / Production host: Escherichia coli (E. coli)
References: UniProt: P0C619, UniProt: A5W4F1*PLUS, toluene dioxygenase
#3: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#4: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe

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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: 7.49 Å3/Da
Crystal growTemperature: 286 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 40%(w/v) polyethylene glycol 600, 0.1 M sodium citrate pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 286K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.00895 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 27, 2004 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00895 Å / Relative weight: 1
ReflectionResolution: 3.2→48.147 Å / Num. all: 37553 / Num. obs: 37553 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 9.7 % / Rmerge(I) obs: 0.117 / Rsym value: 0.117 / Net I/σ(I): 5.64
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3.2-3.378.50.631.24546553750.63100
3.37-3.588.90.4541.54543950840.454100
3.58-3.829.60.3032.34626148090.303100
3.82-4.1310.20.213.24593844850.21100
4.13-4.5310.60.1275.34384841510.127100
4.53-5.0610.50.0917.13980337770.091100
5.06-5.8410.50.0748.93516033560.074100
5.84-7.1610.30.06410.42963628790.064100
7.16-10.129.90.04214.22275022880.042100
10.12-48.158.70.03715.41176513490.03798.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.575 / Cor.coef. Fo:Fc: 0.455 / Cor.coef. Io to Ic: 0.354

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.1.20data scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→48.17 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.895 / WRfactor Rfree: 0.235 / WRfactor Rwork: 0.208 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.776 / SU B: 15.594 / SU ML: 0.26 / SU R Cruickshank DPI: 0.461 / SU Rfree: 0.347 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.461 / ESU R Free: 0.347 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1804 5 %RANDOM
Rwork0.245 ---
obs0.246 35910 95.71 %-
all-35910 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 115.96 Å2 / Biso mean: 74.843 Å2 / Biso min: 52.55 Å2
Refinement stepCycle: LAST / Resolution: 3.2→48.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4821 0 5 0 4826
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0214949
X-RAY DIFFRACTIONr_angle_refined_deg1.8621.9326707
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.4285592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.95323.192260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.22115806
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4731546
X-RAY DIFFRACTIONr_chiral_restr0.1310.2699
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023871
X-RAY DIFFRACTIONr_nbd_refined0.2670.22298
X-RAY DIFFRACTIONr_nbtor_refined0.3280.23344
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2151
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2260.2134
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.214
X-RAY DIFFRACTIONr_mcbond_it0.7731.53036
X-RAY DIFFRACTIONr_mcangle_it1.40824769
X-RAY DIFFRACTIONr_scbond_it1.6232210
X-RAY DIFFRACTIONr_scangle_it2.7814.51936
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 133 -
Rwork0.341 2573 -
all-2706 -
obs--98.9 %

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