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- PDB-3rnf: Structure of the Toluene/o-Xylene Monooxygenase Hydroxylase T201S... -

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Basic information

Entry
Database: PDB / ID: 3rnf
TitleStructure of the Toluene/o-Xylene Monooxygenase Hydroxylase T201S/V271A Double Mutant
Components(Toluene o-xylene monooxygenase ...) x 3
KeywordsOXIDOREDUCTASE / toluene / hydroxylase / four-helix bundle / diiron / oxygen pathway
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 / 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
: / Toluene o-xylene monooxygenase component / Toluene o-xylene monooxygenase component / Toluene o-xylene monooxygenase component
Similarity search - Component
Biological speciesPseudomonas sp. OX1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGucinski, G. / Song, W.J. / Lippard, S.J. / Sazinsky, M.H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Tracking a defined route for O2 migration in a dioxygen-activating diiron enzyme.
Authors: Song, W.J. / Gucinski, G. / Sazinsky, M.H. / Lippard, S.J.
History
DepositionApr 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2011Group: Database references
Revision 1.2Sep 21, 2011Group: Database references
Revision 1.3Aug 23, 2017Group: Data collection / Category: diffrn_detector / diffrn_radiation
Item: _diffrn_detector.detector / _diffrn_detector.type / _diffrn_radiation.monochromator
Revision 1.4Sep 13, 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_ref_seq_dif / 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_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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _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 component
B: Toluene o-xylene monooxygenase component
C: Toluene o-xylene monooxygenase component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,5247
Polymers106,1123
Non-polymers4124
Water9,872548
1
A: Toluene o-xylene monooxygenase component
B: Toluene o-xylene monooxygenase component
C: Toluene o-xylene monooxygenase component
hetero molecules

A: Toluene o-xylene monooxygenase component
B: Toluene o-xylene monooxygenase component
C: Toluene o-xylene monooxygenase component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,04814
Polymers212,2246
Non-polymers8248
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12330 Å2
ΔGint-93 kcal/mol
Surface area31500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.340, 183.340, 68.370
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Toluene o-xylene monooxygenase ... , 3 types, 3 molecules ABC

#1: Protein Toluene o-xylene monooxygenase component / toluene/o-xylene monooxygenase hydroxylase alpha subunit


Mass: 57744.633 Da / Num. of mol.: 1 / Mutation: T201S,V271A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. OX1 (bacteria) / Gene: touA / Production host: Escherichia coli (E. coli)
References: UniProt: Q6IV66, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen
#2: Protein Toluene o-xylene monooxygenase component / toluene/o-xylene monooxygenase hydroxylase beta subunit


Mass: 38381.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. OX1 (bacteria) / Gene: touE / Production host: Escherichia coli (E. coli)
References: UniProt: Q6IV62, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen
#3: Protein Toluene o-xylene monooxygenase component / toluene/o-xylene monooxygenase hydroxylase gamma subunit


Mass: 9986.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. OX1 (bacteria) / Gene: touB / Production host: Escherichia coli (E. coli)
References: UniProt: Q6IV65, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen

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Non-polymers , 4 types, 552 molecules

#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 548 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM HEPES, 2.1 mM ammonium sulfate, 2% PEG400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.03
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2010
RadiationMonochromator: Si(111) Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.2→45.835 Å / Num. all: 66756 / Num. obs: 66756 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9 % / Rsym value: 0.1 / Net I/σ(I): 16.4
Reflection shellResolution: 2.2→2.29 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 6.9 / Rsym value: 0.317 / % possible all: 100

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Processing

Software
NameVersionClassification
iMOSFLMdata reduction
MOLREPphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2INC

2inc


Resolution: 2.2→45.835 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.18 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.173 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2004 3372 5.1 %RANDOM
Rwork0.15363 ---
obs0.15597 63335 99.61 %-
all-66758 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.205 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0.05 Å20 Å2
2---0.1 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 2.2→45.835 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7353 0 22 548 7923
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0217581
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8161.9310291
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.15896
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.75423.869398
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.295151242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.621555
X-RAY DIFFRACTIONr_chiral_restr0.1310.21055
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215926
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0451.54487
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.90527214
X-RAY DIFFRACTIONr_scbond_it3.45633094
X-RAY DIFFRACTIONr_scangle_it5.2594.53077
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 262 -
Rwork0.208 4610 -
obs--99.98 %

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