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- PDB-1t0s: Structure of the Toluene/o-Xylene Monooxygenase Hydroxylase with ... -

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Basic information

Entry
Database: PDB / ID: 1t0s
TitleStructure of the Toluene/o-Xylene Monooxygenase Hydroxylase with 4-bromophenol bound
Components
  • (toluene, o-xylene monooxygenase oxygenase ...) x 2
  • touB
KeywordsOXIDOREDUCTASE / diiron / 4-bromophenol / channel / 4-helix bundle / carboxylate bridge
Function / homology
Function and homology information


oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / cellular aromatic compound metabolic process / monooxygenase activity / metal ion binding
Similarity search - Function
YHS domain / YHS domain / TmoB-like / Toluene-4-monooxygenase system B / TmoB-like superfamily / Toluene-4-monooxygenase system protein B (TmoB) / Methane/phenol monooxygenase, hydroxylase component / Propane/methane/phenol/toluene hydroxylase / Methane/Phenol/Alkene Hydroxylase / Ribonucleotide Reductase, subunit A ...YHS domain / YHS domain / TmoB-like / Toluene-4-monooxygenase system B / TmoB-like superfamily / Toluene-4-monooxygenase system protein B (TmoB) / Methane/phenol monooxygenase, hydroxylase component / Propane/methane/phenol/toluene hydroxylase / Methane/Phenol/Alkene Hydroxylase / Ribonucleotide Reductase, subunit A / Ribonucleotide Reductase, subunit A / Ribonucleotide reductase-like / Ferritin-like superfamily / Ubiquitin-like (UB roll) / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
4-BROMOPHENOL / : / SULFANYLACETIC ACID / HYDROXIDE ION / Toluene o-xylene monooxygenase oxygenase subunit TouA / Toluene o-xylene monooxygenase component TouB / Toluene o-xylene monooxygenase component TouE
Similarity search - Component
Biological speciesPseudomonas stutzeri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSazinsky, M.H. / Bard, J. / Di Donato, A. / Lippard, S.J.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Crystal Structure of the Toluene/o-Xylene Monooxygenase Hydroxylase from Pseudomonas stutzeri OX1: INSIGHT INTO THE SUBSTRATE SPECIFICITY, SUBSTRATE CHANNELING, AND ACTIVE SITE TUNING OF ...Title: Crystal Structure of the Toluene/o-Xylene Monooxygenase Hydroxylase from Pseudomonas stutzeri OX1: INSIGHT INTO THE SUBSTRATE SPECIFICITY, SUBSTRATE CHANNELING, AND ACTIVE SITE TUNING OF MULTICOMPONENT MONOOXYGENASES.
Authors: Sazinsky, M.H. / Bard, J. / Di Donato, A. / Lippard, S.J.
History
DepositionApr 12, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: toluene, o-xylene monooxygenase oxygenase subunit
B: toluene, o-xylene monooxygenase oxygenase subunit
C: touB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,41313
Polymers106,1543
Non-polymers1,25910
Water4,810267
1
A: toluene, o-xylene monooxygenase oxygenase subunit
B: toluene, o-xylene monooxygenase oxygenase subunit
C: touB
hetero molecules

A: toluene, o-xylene monooxygenase oxygenase subunit
B: toluene, o-xylene monooxygenase oxygenase subunit
C: touB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,82626
Polymers212,3086
Non-polymers2,51820
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13890 Å2
ΔGint-74 kcal/mol
Surface area30870 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)183.242, 183.242, 67.671
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-424-

HOH

DetailsThe biological homodimer is generated by the two fold axis -x, y-x, -2/3-z

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Components

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Toluene, o-xylene monooxygenase oxygenase ... , 2 types, 2 molecules AB

#1: Protein toluene, o-xylene monooxygenase oxygenase subunit /


Mass: 57786.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ALPHA SUBUNIT / Source: (gene. exp.) Pseudomonas stutzeri (bacteria) / Gene: touA / Plasmid: peT22BEA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O87798
#2: Protein toluene, o-xylene monooxygenase oxygenase subunit /


Mass: 38381.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: BETA SUBUNIT / Source: (gene. exp.) Pseudomonas stutzeri (bacteria) / Gene: touE / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O87802

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Protein , 1 types, 1 molecules C

#3: Protein touB


Mass: 9986.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GAMMA SUBUNIT / Source: (gene. exp.) Pseudomonas stutzeri (bacteria) / Gene: touB / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O87799

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Non-polymers , 5 types, 277 molecules

#4: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#5: Chemical ChemComp-OH / HYDROXIDE ION / Hydroxide


Mass: 17.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: HO
#6: Chemical ChemComp-MCR / SULFANYLACETIC ACID / MERCAPTOACETIC ACID / Thioglycolic acid


Mass: 92.117 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2S
#7: Chemical
ChemComp-BML / 4-BROMOPHENOL / Bromophenol


Mass: 173.007 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H5BrO
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 1.46 Å3/Da / Density % sol: 16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 400, HEPES, ammonium sulfate, glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.127 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 10, 2003
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 66417 / Num. obs: 65354 / % possible obs: 98.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Biso Wilson estimate: 31.7 Å2 / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 21.4
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 4.1 / Rsym value: 0.352 / % possible all: 86.4

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→29.47 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 370444.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.273 2301 4.3 %RANDOM
Rwork0.236 ---
all0.236 66417 --
obs0.236 53610 98.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.1475 Å2 / ksol: 0.347831 e/Å3
Displacement parametersBiso mean: 50 Å2
Baniso -1Baniso -2Baniso -3
1--6.72 Å20.02 Å20 Å2
2---6.72 Å20 Å2
3---13.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.2→29.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7344 0 56 267 7667
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.31.5
X-RAY DIFFRACTIONc_mcangle_it2.12
X-RAY DIFFRACTIONc_scbond_it2.122
X-RAY DIFFRACTIONc_scangle_it3.042.5
LS refinement shellResolution: 2.2→2.35 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rwork0.314 8618 -
obs--84.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION4BRPHENOL.PARAMBRPHENOL.TOP

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