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- PDB-3ge3: Crystal Structure of the reduced Toluene 4-Monooxygenase HD T201A... -

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Basic information

Entry
Database: PDB / ID: 3ge3
TitleCrystal Structure of the reduced Toluene 4-Monooxygenase HD T201A mutant complex
Components(Toluene-4-monooxygenase system protein ...) x 4
KeywordsOXIDOREDUCTASE / DIIRON HYDROXYLASE / EFFECTOR PROTEIN / 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: 1.52 Å
AuthorsElsen, N.L. / Bailey, L.J. / 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 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 2, 2014Group: Structure summary
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_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
Revision 1.4Sep 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,0098
Polymers117,8034
Non-polymers2064
Water16,322906
1
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

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)236,01816
Polymers235,6058
Non-polymers4128
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area33760 Å2
ΔGint-246 kcal/mol
Surface area62170 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15080 Å2
ΔGint-119 kcal/mol
Surface area32880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.260, 115.966, 180.137
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe second part of the biological assembly is generated by the two fold axis: x, -y,-z

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Components

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Toluene-4-monooxygenase system protein ... , 4 types, 4 molecules ABCE

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


Mass: 58139.312 Da / Num. of mol.: 1 / Mutation: T201A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas mendocina (bacteria) / Gene: tmoA / Plasmid: p58K_ABE_T201A / Production host: Escherichia coli (E. coli) / 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.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas mendocina (bacteria) / Gene: tmoE / Production host: Escherichia coli (E. coli)
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.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas mendocina (bacteria) / Gene: tmoB / Production host: Escherichia coli (E. coli)
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.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas mendocina (bacteria) / Gene: tmoD / Production host: Escherichia coli (E. coli)
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 , 4 types, 910 molecules

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


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 906 / 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: 44.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG 3350, 200 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-D / Wavelength: 0.97924 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 19, 2008
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.52→30.6 Å / Num. all: 150546 / Num. obs: 159683 / % possible obs: 99.35 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.071
Reflection shellHighest resolution: 1.52 Å / % possible all: 99.35

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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: 1.52→30.6 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.141 / SU ML: 0.043 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.075 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19302 7875 5 %Test set from 3DHH
Rwork0.16818 ---
all0.16939 151531 --
obs0.16939 150546 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.932 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å20 Å2
2--0.21 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.52→30.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8027 0 7 906 8940
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0218601
X-RAY DIFFRACTIONr_angle_refined_deg1.5321.93211725
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.75151051
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.12124.137452
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.713151448
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4591558
X-RAY DIFFRACTIONr_chiral_restr0.0660.21196
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0216832
X-RAY DIFFRACTIONr_mcbond_it0.9161.55124
X-RAY DIFFRACTIONr_mcangle_it1.55928303
X-RAY DIFFRACTIONr_scbond_it2.39533477
X-RAY DIFFRACTIONr_scangle_it3.6454.53420
LS refinement shellResolution: 1.523→1.562 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 588 -
Rwork0.244 10789 -
obs--97.09 %

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