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- PDB-2inc: Native Toluene/o-xylene Monooxygenase Hydroxylase X-ray Crystal S... -

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Basic information

Entry
Database: PDB / ID: 2inc
TitleNative Toluene/o-xylene Monooxygenase Hydroxylase X-ray Crystal Structure
Components
  • (Toluene, o-xylene monooxygenase oxygenase ...) x 2
  • TouB protein
KeywordsOXIDOREDUCTASE / diiron / 4-helix bundle / carboxylate bridge / metalloenzyme
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 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: 1.85 Å
AuthorsMcCormick, M.S. / Sazinsky, M.H. / Condon, K.L. / Lippard, S.J.
CitationJournal: J.Am.Chem.Soc. / Year: 2006
Title: X-ray crystal structures of manganese(II)-reconstituted and native toluene/o-xylene monooxygenase hydroxylase reveal rotamer shifts in conserved residues and an enhanced view of the protein interior.
Authors: McCormick, M.S. / Sazinsky, M.H. / Condon, K.L. / Lippard, S.J.
History
DepositionOct 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 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_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.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 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,5426
Polymers104,1483
Non-polymers3943
Water6,575365
1
A: Toluene, o-xylene monooxygenase oxygenase subunit
B: Toluene, o-xylene monooxygenase oxygenase subunit
C: TouB protein
hetero molecules

A: Toluene, o-xylene monooxygenase oxygenase subunit
B: Toluene, o-xylene monooxygenase oxygenase subunit
C: TouB protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,08412
Polymers208,2966
Non-polymers7886
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Unit cell
Length a, b, c (Å)182.555, 182.555, 68.111
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe second half of the dimeric biological assembly is generated by the two fold axis: x-y, -y, -z+2/3

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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: 57039.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas stutzeri (bacteria) / Strain: OX1 / Gene: touA / 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 / Toluene o-xylene monooxygenase component


Mass: 37438.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas stutzeri (bacteria) / Strain: OX1 / 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 protein / Toluene o-xylene monooxygenase component


Mass: 9670.053 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas stutzeri (bacteria) / Strain: OX1 / 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 , 3 types, 368 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-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 3.14 Å3/Da / Density % sol: 60.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM HEPES pH 7.5, 2.1-2.5 M ammonium sulfate, 2-4% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 101 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 6, 2006
Details: Flat collimating mirror, double crystal monochromator, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 99695 / Num. obs: 96823 / % possible obs: 90.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.087 / Net I/σ(I): 55.8
Reflection shellResolution: 1.85→1.92 Å / Mean I/σ(I) obs: 5.5 / Rsym value: 0.43 / % possible all: 78.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1T0Q

1t0q


Resolution: 1.85→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.348 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.132 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23 4813 5 %RANDOM
Rwork0.197 ---
all0.199 99695 --
obs0.199 96823 90.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.727 Å2
Baniso -1Baniso -2Baniso -3
1--3.33 Å2-1.66 Å20 Å2
2---3.33 Å20 Å2
3---4.99 Å2
Refinement stepCycle: LAST / Resolution: 1.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7335 0 21 365 7721
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0217563
X-RAY DIFFRACTIONr_angle_refined_deg1.6891.9310268
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6585893
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.32623.854397
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.426151240
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5271555
X-RAY DIFFRACTIONr_chiral_restr0.1590.21053
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025918
X-RAY DIFFRACTIONr_nbd_refined0.2160.23878
X-RAY DIFFRACTIONr_nbtor_refined0.3150.25221
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2468
X-RAY DIFFRACTIONr_metal_ion_refined0.1440.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.27
X-RAY DIFFRACTIONr_mcbond_it1.0731.54570
X-RAY DIFFRACTIONr_mcangle_it1.73427194
X-RAY DIFFRACTIONr_scbond_it2.75933503
X-RAY DIFFRACTIONr_scangle_it4.2474.53074
LS refinement shellResolution: 1.852→1.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 270 -
Rwork0.282 5807 -
obs-6077 98.88 %

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