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

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Basic information

Entry
Database: PDB / ID: 3rna
TitleStructure of the Toluene/o-Xylene Monooxygenase Hydroxylase T201S/I100W 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
: / HYDROXIDE ION / 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: 3 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 1.3Sep 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_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_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)106,3426
Polymers106,2133
Non-polymers1293
Water84747
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)212,68412
Polymers212,4266
Non-polymers2576
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11470 Å2
ΔGint-97 kcal/mol
Surface area31540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.793, 182.793, 67.701
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: 57845.734 Da / Num. of mol.: 1 / Mutation: T201S,I100W
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 , 3 types, 50 molecules

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


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


Mass: 17.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: HO
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 3.07 Å3/Da / Density % sol: 59.99 %
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: APS / Beamline: 24-ID-E / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 30, 2010
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.998→45.698 Å / Num. all: 24140 / Num. obs: 24140 / % possible obs: 96.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Rsym value: 0.103 / Net I/σ(I): 30.1
Reflection shellResolution: 2.998→3.07 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 9 / Rsym value: 0.26 / % possible all: 97.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2INC

2inc


Resolution: 3→45.698 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.899 / SU B: 15.697 / SU ML: 0.285 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.412 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24108 1283 5 %RANDOM
Rwork0.17726 ---
obs0.18046 24140 96.68 %-
all-24140 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.981 Å2
Baniso -1Baniso -2Baniso -3
1--6.1 Å2-3.05 Å20 Å2
2---6.1 Å20 Å2
3---9.15 Å2
Refinement stepCycle: LAST / Resolution: 3→45.698 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7340 0 3 47 7390
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0217552
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6571.92710261
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1935893
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.45123.844398
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.037151239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6631555
X-RAY DIFFRACTIONr_chiral_restr0.1210.21051
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215920
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_it0.6051.54472
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.20127192
X-RAY DIFFRACTIONr_scbond_it1.8133080
X-RAY DIFFRACTIONr_scangle_it3.074.53069
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.076 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 73 -
Rwork0.254 1767 -
obs--95.58 %

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