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- PDB-1wql: Cumene dioxygenase (cumA1A2) from Pseudomonas fluorescens IP01 -

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Basic information

Entry
Database: PDB / ID: 1wql
TitleCumene dioxygenase (cumA1A2) from Pseudomonas fluorescens IP01
Components
  • ethylbenzene dioxygenase small subunit
  • iron-sulfur protein large subunit of cumene dioxygenase
KeywordsOXIDOREDUCTASE / biphenyl dioxygenase / cumene dioxygenase / naphthalene dioxygenase / polychlorinated biphenyl degradation / Rieske non-heme iron dioxygenase
Function / homology
Function and homology information


: / dioxygenase activity / 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 / OXYGEN MOLECULE / Iron-sulfur protein large subunit of cumene dioxygenase / Ethylbenzene dioxygenase small subunit
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDong, X. / Fushinobu, S. / Fukuda, E. / Terada, T. / Nakamura, S. / Shimizu, K. / Nojiri, H. / Omori, T. / Shoun, H. / Wakagi, T.
CitationJournal: J.BACTERIOL. / Year: 2005
Title: Crystal Structure of the Terminal Oxygenase Component of Cumene Dioxygenase from Pseudomonas fluorescens IP01
Authors: Dong, X. / Fushinobu, S. / Fukuda, E. / Terada, T. / Nakamura, S. / Shimizu, K. / Nojiri, H. / Omori, T. / Shoun, H. / Wakagi, T.
History
DepositionSep 30, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 29, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 25, 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 / 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: iron-sulfur protein large subunit of cumene dioxygenase
B: ethylbenzene dioxygenase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,2625
Polymers73,9982
Non-polymers2643
Water8,503472
1
A: iron-sulfur protein large subunit of cumene dioxygenase
B: ethylbenzene dioxygenase small subunit
hetero molecules

A: iron-sulfur protein large subunit of cumene dioxygenase
B: ethylbenzene dioxygenase small subunit
hetero molecules

A: iron-sulfur protein large subunit of cumene dioxygenase
B: ethylbenzene dioxygenase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,78615
Polymers221,9956
Non-polymers7919
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area32760 Å2
ΔGint-200 kcal/mol
Surface area56450 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)147.036, 147.036, 147.036
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11B-278-

HOH

DetailsThe biological assembly is a hexamer generated from the dimer in the asymmetric unit by the operations: z, x, y and y, z, x.

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein iron-sulfur protein large subunit of cumene dioxygenase / / cumene dioxygenase large subunit


Mass: 52357.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: CUMA1 / Plasmid: pUC118 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: Q51743, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of two atoms of oxygen into the other donor
#2: Protein ethylbenzene dioxygenase small subunit / cumene dioxygenase small subunit


Mass: 21640.428 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: CUMA2 / Plasmid: pUC118 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: Q51744, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of two atoms of oxygen into the other donor

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Non-polymers , 4 types, 475 molecules

#3: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#5: Chemical ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 472 / 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: 3.5 Å3/Da / Density % sol: 65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.1
Details: PEG 3350, tri-lithium citrate tetrahydrate, pH 8.1, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 18, 2002
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 53921 / Num. obs: 53807 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.5 % / Biso Wilson estimate: 12.8 Å2 / Rsym value: 0.113 / Net I/σ(I): 17.7
Reflection shellResolution: 2.2→2.28 Å / Mean I/σ(I) obs: 6.5 / Num. unique all: 5317 / Rsym value: 0.295 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EG9

1eg9


Resolution: 2.2→19.65 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3753443.73 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.196 2678 5 %RANDOM
Rwork0.173 ---
all0.174 53807 --
obs0.173 53762 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.7029 Å2 / ksol: 0.373348 e/Å3
Displacement parametersBiso mean: 21.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4994 0 7 472 5473
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_mcbond_it1.671.5
X-RAY DIFFRACTIONc_mcangle_it2.332
X-RAY DIFFRACTIONc_scbond_it2.792
X-RAY DIFFRACTIONc_scangle_it3.732.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.221 450 5.1 %
Rwork0.183 8445 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4FESO2.PARAMFESO2.TOP

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