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- PDB-3i63: Peroxide Bound Toluene 4-Monooxygenase -

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Basic information

Entry
Database: PDB / ID: 3i63
TitlePeroxide Bound Toluene 4-Monooxygenase
Components(Toluene-4-monooxygenase system protein ...) x 4
KeywordsOXIDOREDUCTASE / Peroxide / T4MOH / diiron hydroxylase / monooxygenase / Aromatic hydrocarbons catabolism / FAD / Flavoprotein / Iron
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
: / HYDROGEN PEROXIDE / 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: 2.09 Å
AuthorsBailey, L.J. / Fox, B.G.
CitationJournal: Biochemistry / Year: 2009
Title: Crystallographic and catalytic studies of the peroxide-shunt reaction in a diiron hydroxylase.
Authors: Bailey, L.J. / Fox, B.G.
History
DepositionJul 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.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_seq_id / _struct_conn.ptnr1_label_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_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-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)118,0128
Polymers117,8334
Non-polymers1804
Water11,061614
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)236,02516
Polymers235,6658
Non-polymers3598
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area33190 Å2
ΔGint-212 kcal/mol
Surface area62500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.792, 116.929, 181.608
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-581-

HOH

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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: 58169.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas mendocina (bacteria) / Strain: KR1 / Gene: tmoA / Production host: Escherichia coli (E. coli)
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) / Strain: KR1 / 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) / Strain: KR1 / 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) / Strain: KR1 / 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 , 3 types, 618 molecules

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


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#6: Chemical ChemComp-PEO / HYDROGEN PEROXIDE / Hydrogen peroxide


Mass: 34.015 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 614 / 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: 2.23 Å3/Da / Density % sol: 44.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: .1 M Bis-Tris, 200 mM Ammonium Acetate, 24% PEG 3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97872 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Dec 11, 2008
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.09→49.4 Å / Num. all: 58358 / Num. obs: 58829 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1
Reflection shellResolution: 2.09→2.14 Å

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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 / Resolution: 2.09→49.4 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / SU B: 8.351 / SU ML: 0.105 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.201 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20116 3143 5.1 %RANDOM
Rwork0.15639 ---
all0.15871 59303 --
obs0.15871 58829 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.496 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20 Å2
2--0.09 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.09→49.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7994 0 6 614 8614
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0218344
X-RAY DIFFRACTIONr_angle_refined_deg1.8371.92911351
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.63851003
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.77124.045440
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.822151390
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8921557
X-RAY DIFFRACTIONr_chiral_restr0.0070.21171
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0216555
X-RAY DIFFRACTIONr_mcbond_it1.0341.54951
X-RAY DIFFRACTIONr_mcangle_it1.68227996
X-RAY DIFFRACTIONr_scbond_it3.05433393
X-RAY DIFFRACTIONr_scangle_it4.4474.53349
LS refinement shellResolution: 2.09→2.144 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.213 212 -
Rwork0.154 4013 -
obs--92.59 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.57050.0534-0.1520.2023-0.19211.36560.01250.1323-0.036-0.00860.09210.0906-0.0569-0.203-0.10460.1095-0.006-0.01420.07330.02120.124-27.5118.181-22.255
210.58316.9359-7.71934.5664-5.10265.73180.6815-0.45790.4460.5392-0.38620.2754-0.71080.434-0.29540.464-0.165-0.0470.54120.05490.22385.4529.1772.461
31.1171-0.18130.1170.3946-0.56691.44090.0362-0.02190.03050.09340.00490.0327-0.30180.1535-0.04120.1528-0.04550.00330.0427-0.00730.0736-12.97714.97-15.191
40.88810.40640.23180.9299-0.0371.40440.0912-0.02240.02820.1912-0.0605-0.0648-0.29610.308-0.03080.2026-0.11240.00090.092-0.00050.0433-6.10821.92-17.732
50.8870.0740.27220.5395-0.20321.8941-0.0041-0.00030.01090.0047-0.0513-0.0014-0.12460.32550.05550.1023-0.02350.00180.0925-0.00460.0599-6.4425.926-17.321
66.02190.85211.97361.31170.17362.82130.02580.1587-0.0159-0.059-0.03990.0568-0.09690.11350.01420.0958-0.04520.0090.09-0.00130.0363-9.45113.671-35.665
70.63190.1681-0.27090.8896-0.29830.72690.0160.00550.0167-0.0011-0.1297-0.1645-0.05620.45530.11360.0565-0.0626-0.00640.37360.06080.0710.82411.217-25.076
80.7257-0.82770.16210.9715-0.14291.54910.02620.04870.16680.0207-0.0848-0.2056-0.40810.41910.05850.2242-0.2097-0.02120.20660.0430.10686.63927.912-32.358
93.42572.84180.06576.88190.13158.20570.0004-0.18110.21610.12710.0373-0.2653-0.32760.2692-0.03760.3734-0.2418-0.00570.1827-0.03410.13035.87239.947-19.438
102.4729-4.15350.82299.47361.61016.8087-0.8174-0.17960.58781.81340.3921-1.0532-0.99551.37120.42520.8149-0.4623-0.29240.65490.09920.254415.25923.121-8.528
1110.0221-0.66331.76335.4445-0.56170.69490.0107-0.62151.09620.6724-0.12320.0559-0.32450.07840.11250.5972-0.21940.03760.2363-0.08260.2839-5.17729.343.346
120.59730.0237-0.05250.4748-0.31861.39570.0594-0.04070.1460.17950.02710.0728-0.49980.1099-0.08660.2931-0.03340.03870.0181-0.01330.1025-19.04727.06-12.367
131.37210.48220.15230.8849-0.4153.1074-0.02160.0032-0.09320.12910.1760.24090.2138-0.752-0.15450.0969-0.05940.02420.22180.0770.1418-47.346-1.591-10.201
140.83770.3364-0.19950.8438-0.31381.40070.03080.1130.12550.06120.16440.2013-0.2257-0.4615-0.19510.10160.07810.01970.15880.08420.1134-39.52915.479-18.075
151.01120.6726-0.08051.7718-0.48291.57740.1903-0.11180.18920.38730.02070.2441-0.495-0.4008-0.21090.26820.14050.12660.14030.03530.1698-38.34822.901-5.888
167.64087.03-0.85959.97960.0762.14080.07270.06280.54340.16410.11950.7569-0.3033-0.5512-0.19230.13330.15750.0280.23840.1030.195-49.00625.595-17.38
172.4762-2.48212.00292.5535-2.21262.8506-0.20760.13530.70340.2328-0.167-0.6089-0.64020.7290.37470.3073-0.373-0.08940.46570.0720.382120.7335.954-31.416
182.5657-1.9508-1.26824.1161-2.47876.41470.07730.10820.5651-0.0665-0.2235-0.8733-0.44880.92920.14610.1751-0.31290.00650.59210.06560.362826.25829.769-34.684
197.85280.9426-0.54742.4576-1.35070.83760.32051.42170.6179-0.5928-0.8639-0.22960.29110.68520.54350.6866-0.12580.13411.390.51790.847322.43737.579-43.993
204.6636-1.46332.64073.5593-3.09543.3621-0.00710.78390.08950.0675-0.497-0.7572-0.35670.79880.50410.4931-0.37470.02640.60250.1660.366119.03336.056-39.967
217.61040.6309-5.074120.07482.65213.8561-0.46510.1624-0.5799-1.00690.2148-0.77280.1638-0.0560.25040.34510.10270.02830.5325-0.0310.21854.098-2.083-38.001
221.31950.55280.34291.6496-0.60492.11340.0340.0352-0.1438-0.0953-0.014-0.09890.51380.2588-0.02010.17810.0649-0.00310.1015-0.01640.0691-8.281-11.97-19.708
234.93954.41873.80677.99757.341310.0834-0.00110.1791-0.39720.12060.1611-0.38040.71020.8511-0.15990.17910.12370.03220.16050.0170.0658-0.432-10.33-20.887
243.59361.87044.41766.09923.0649.63610.10260.1257-0.0975-0.0301-0.16130.07470.83450.38020.05870.14150.05530.01430.1108-0.00520.0671-5.426-8.716-24.93
254.9605-0.5699-2.93770.9507-0.01710.0985-0.02870.0939-0.14510.14390.08780.13210.5501-0.3825-0.05910.2048-0.0312-0.03690.0433-0.01070.1076-17.354-15.969-17.436
260.42610.5588-0.8591.7151-1.37723.39530.00270.1034-0.0374-0.04930.1230.12720.2547-0.1956-0.12580.11370.0053-0.02510.0797-0.00170.0861-17.301-7.665-18.541
273.4089-2.3452-3.09916.36490.319913.81820.02720.32150.0291-0.6734-0.0676-0.09090.18470.3040.04040.2425-0.094-0.00760.3279-0.0350.1101-11.548-6.138-37.215
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 76
2X-RAY DIFFRACTION2A77 - 85
3X-RAY DIFFRACTION3A86 - 146
4X-RAY DIFFRACTION4A147 - 195
5X-RAY DIFFRACTION5A196 - 241
6X-RAY DIFFRACTION6A242 - 272
7X-RAY DIFFRACTION7A273 - 381
8X-RAY DIFFRACTION8A382 - 451
9X-RAY DIFFRACTION9A452 - 470
10X-RAY DIFFRACTION10A471 - 492
11X-RAY DIFFRACTION11B4 - 20
12X-RAY DIFFRACTION12B21 - 90
13X-RAY DIFFRACTION13B91 - 120
14X-RAY DIFFRACTION14B121 - 239
15X-RAY DIFFRACTION15B240 - 284
16X-RAY DIFFRACTION16B285 - 307
17X-RAY DIFFRACTION17C3 - 40
18X-RAY DIFFRACTION18C41 - 55
19X-RAY DIFFRACTION19C56 - 68
20X-RAY DIFFRACTION20C69 - 84
21X-RAY DIFFRACTION21E3 - 10
22X-RAY DIFFRACTION22E11 - 37
23X-RAY DIFFRACTION23E38 - 47
24X-RAY DIFFRACTION24E48 - 56
25X-RAY DIFFRACTION25E57 - 66
26X-RAY DIFFRACTION26E67 - 97
27X-RAY DIFFRACTION27E98 - 103

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