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- PDB-3n1x: X-ray Crystal Structure of Toluene/o-Xylene Monooxygenase Hydroxy... -

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Basic information

Entry
Database: PDB / ID: 3n1x
TitleX-ray Crystal Structure of Toluene/o-Xylene Monooxygenase Hydroxylase T201C Mutant
Components(Toluene o-xylene monooxygenase ...) x 3
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
: / HYDROXIDE ION / Toluene o-xylene monooxygenase component / Toluene o-xylene monooxygenase component / Toluene o-xylene monooxygenase component
Similarity search - Component
Biological speciesPseudomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSazinsky, M.H. / McCormick, M.S. / Lippard, S.J.
CitationJournal: J.Am.Chem.Soc. / Year: 2010
Title: Active Site Threonine Facilitates Proton Transfer during Dioxygen Activation at the Diiron Center of Toluene/o-Xylene Monooxygenase Hydroxylase.
Authors: Song, W.J. / McCormick, M.S. / Behan, R.K. / Sazinsky, M.H. / Jiang, W. / Lin, J. / Krebs, C. / Lippard, S.J.
History
DepositionMay 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Sep 6, 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.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

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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)106,4438
Polymers106,1563
Non-polymers2875
Water2,522140
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)212,88616
Polymers212,3126
Non-polymers57410
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation2_565-y,x-y+1,z+1/31
crystal symmetry operation6_565-x,-x+y+1,-z+1/31
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11890 Å2
ΔGint-104 kcal/mol
Surface area32040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.294, 183.294, 68.128
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 alpha subunit


Mass: 57788.680 Da / Num. of mol.: 1 / Mutation: T201C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: OX1 / Gene: touA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6IV66
#2: Protein Toluene o-xylene monooxygenase component / Toluene/o-xylene monooxygenase beta subunit


Mass: 38381.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: OX1 / Gene: touE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6IV62
#3: Protein Toluene o-xylene monooxygenase component / Toluene/o-xylene monooxygenase gamma subunit


Mass: 9986.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: OX1 / Gene: touB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6IV65

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Non-polymers , 5 types, 145 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: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 3.11 Å3/Da / Density % sol: 60.48 %
Crystal growTemperature: 293 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 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 11, 2008 / Details: Rh coated flat mirror
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degrees
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 48929 / Num. obs: 48523 / % possible obs: 99.17 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.4→2.462 Å / % possible all: 96.16

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Processing

Software
NameClassification
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2INC

2inc


Resolution: 2.4→38.02 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2425 2592 -Random
Rwork0.18354 ---
obs0.18658 48523 99.17 %-
all-48929 --
Refinement stepCycle: LAST / Resolution: 2.4→38.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7362 0 12 140 7514
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.031
X-RAY DIFFRACTIONr_angle_refined_deg2.839

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