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- PDB-3ge8: Toluene 4-monooxygenase HD T201A diferric, resting state complex -

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Basic information

Entry
Database: PDB / ID: 3ge8
TitleToluene 4-monooxygenase HD T201A diferric, resting state complex
Components(Toluene-4-monooxygenase system protein ...) x 4
KeywordsOXIDOREDUCTASE / DIIRON HYDROXYLASE / EFFECTOR PROTEIN / T4MOH / T201A / Aromatic hydrocarbons catabolism / FAD / Flavoprotein / Iron / Monooxygenase
Function / homology
Function and homology information


toluene 4-monooxygenase / toluene 4-monooxygenase activity / toluene catabolic process / monooxygenase activity / metal ion binding
Similarity search - Function
Monooxygenase component MmoB/DmpM / Phenol Hydroxylase P2 Protein / TmoB-like / Toluene-4-monooxygenase system B / TmoB-like superfamily / Toluene-4-monooxygenase system protein B (TmoB) / Monooxygenase component MmoB/DmpM / Monooxygenase component MmoB/DmpM superfamily / MmoB/DmpM family / Methane/phenol monooxygenase, hydroxylase component ...Monooxygenase component MmoB/DmpM / Phenol Hydroxylase P2 Protein / TmoB-like / Toluene-4-monooxygenase system B / TmoB-like superfamily / Toluene-4-monooxygenase system protein B (TmoB) / Monooxygenase component MmoB/DmpM / Monooxygenase component MmoB/DmpM superfamily / MmoB/DmpM family / 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 / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / : / Toluene-4-monooxygenase system, hydroxylase component subunit alpha / Toluene-4-monooxygenase system, hydroxylase component subunit gamma / Toluene-4-monooxygenase system, effector component / Toluene-4-monooxygenase system, hydroxylase component subunit beta / Toluene-4-monooxygenase system, hydroxylase component subunit alpha
Similarity search - Component
Biological speciesPseudomonas mendocina (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsElsen, N.L. / Bailey, L.J. / Hauser, A.D. / Fox, B.G.
CitationJournal: Biochemistry / Year: 2009
Title: Role for threonine 201 in the catalytic cycle of the soluble diiron hydroxylase toluene 4-monooxygenase.
Authors: Elsen, N.L. / Bailey, L.J. / Hauser, A.D. / Fox, B.G.
History
DepositionFeb 25, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Toluene-4-monooxygenase system protein A
B: Toluene-4-monooxygenase system protein E
C: Toluene-4-monooxygenase system protein B
E: Toluene-4-monooxygenase system protein D
D: Toluene-4-monooxygenase system protein A
F: Toluene-4-monooxygenase system protein E
G: Toluene-4-monooxygenase system protein B
H: Toluene-4-monooxygenase system protein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,94714
Polymers235,6058
Non-polymers3416
Water25,9961443
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33620 Å2
ΔGint-229 kcal/mol
Surface area62380 Å2
MethodPISA
2
A: Toluene-4-monooxygenase system protein A
B: Toluene-4-monooxygenase system protein E
C: Toluene-4-monooxygenase system protein B
E: Toluene-4-monooxygenase system protein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,9737
Polymers117,8034
Non-polymers1713
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15050 Å2
ΔGint-112 kcal/mol
Surface area33050 Å2
MethodPISA
3
D: Toluene-4-monooxygenase system protein A
F: Toluene-4-monooxygenase system protein E
G: Toluene-4-monooxygenase system protein B
H: Toluene-4-monooxygenase system protein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,9737
Polymers117,8034
Non-polymers1713
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14920 Å2
ΔGint-111 kcal/mol
Surface area32970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.288, 115.388, 180.927
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Toluene-4-monooxygenase system protein ... , 4 types, 8 molecules ADBFCGEH

#1: Protein Toluene-4-monooxygenase system protein A


Mass: 58139.312 Da / Num. of mol.: 2 / Mutation: T201A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas mendocina (bacteria) / Strain: KR1 / Gene: tmoA / Plasmid: p58K_ABE_T201A / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q6Q8Q7, UniProt: Q00456*PLUS, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of ...References: UniProt: Q6Q8Q7, UniProt: Q00456*PLUS, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor
#2: Protein Toluene-4-monooxygenase system protein E


Mass: 38433.262 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas mendocina (bacteria) / Strain: KR1 / Gene: tmoE / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q00460, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor
#3: Protein Toluene-4-monooxygenase system protein B


Mass: 9600.989 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas mendocina (bacteria) / Strain: KR1 / Gene: tmoB / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q00457, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor
#4: Protein Toluene-4-monooxygenase system protein D


Mass: 11629.032 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas mendocina (bacteria) / Gene: tmoD / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q00459, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor

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Non-polymers , 3 types, 1449 molecules

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


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1443 / 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: 2.22 Å3/Da / Density % sol: 44.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG 3350, 200 mM Na Acetate, 100 mM Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97926 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Apr 17, 2008
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 115810 / Num. obs: 108513 / % possible obs: 93.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellHighest resolution: 2.19 Å / % possible all: 99.65

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0066refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DHH

3dhh


Resolution: 2.19→47.17 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.916 / SU B: 4.779 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.264 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22924 5414 5 %RANDOM
Rwork0.16063 ---
obs0.16406 102959 99.65 %-
all-103321 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.187 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20 Å2
2--0.18 Å20 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 2.19→47.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16166 0 12 1443 17621
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.02116644
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7831.9322618
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.51351989
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.89424.007876
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.519152772
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.94915115
X-RAY DIFFRACTIONr_chiral_restr0.0140.22326
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02113055
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_it1.051.59888
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.84215938
X-RAY DIFFRACTIONr_scbond_it3.12236756
X-RAY DIFFRACTIONr_scangle_it4.6874.56675
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.188→2.244 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 370 -
Rwork0.153 7187 -
obs--95.57 %

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