PDB-3i5j: Diferric Resting State Toluene 4-Monooxygenase HD complex

ID or keywords:

Entry

Database: PDB / ID: 3i5j

Title

Diferric Resting State Toluene 4-Monooxygenase HD complex

Components

(Toluene-4-monooxygenase system protein ...) x 4

Keywords

OXIDOREDUCTASE / Hydroxylase / Toluene 4-Monooxygenase / monooxygenase / peroxide / 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

Biological species

Pseudomonas mendocina (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Bailey, L.J. / Fox, B.G.

Citation

Journal: 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

Deposition	Jul 5, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 13, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.2	Feb 21, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3i5j.cif.gz	229.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3i5j.ent.gz	182.1 KB	Display	PDB format
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Validation report

Summary document	3i5j_validation.pdf.gz	456.2 KB	Display	wwPDB validaton report
Full document	3i5j_full_validation.pdf.gz	475.5 KB	Display
Data in XML	3i5j_validation.xml.gz	44.6 KB	Display
Data in CIF	3i5j_validation.cif.gz	65.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/i5/3i5j ftp://data.pdbj.org/pub/pdb/validation_reports/i5/3i5j	HTTPS FTP

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Related structure data

Related structure data	3i63C 3dhh 3dhi C: citing same article (ref.)
Similar structure data	3q3o-1 3ri7-1 3q3n-1 3i63-1 5tdu-1 3q3m-d 7d0k-d 3dhi-3 7d0l-d 3ge8-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#238 - Oct 2019 Ribonucleotide Reductase similarity (1)

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

118 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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

defined by author&software
236 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	100.405, 115.693, 181.307
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-733- HOH

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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) / Gene: tmoA / Production host: Escherichia coli (E. coli) References: UniProt: Q6Q8Q7, UniProt: Q00456PLUS, 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: Q00456PLUS, 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 , 2 types, 695 molecules

#5: Chemical	ChemComp-FE / FE (III) ION Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 693 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.23 Å³/Da / Density % sol: 44.95 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 24% PEG 3350, 200 mM Ammonium Chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
Detector	Type: RAYONIX MX-300 / Detector: CCD / Date: Dec 11, 2008
Radiation	Monochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 1.9→90.54 Å / Num. obs: 83188 / % possible obs: 97.44 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1
Reflection shell	Resolution: 1.9→1.949 Å / % possible all: 86.52

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
MOLREP		phasing
REFMAC	5.5.0066	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.9→90.54 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.943 / SU B: 6.964 / SU ML: 0.092 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20715	4051	5 %	RANDOM
R_work	0.15872	-	-	-
all	0.16114	-	-	-
obs	0.16114	76944	97.44 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 14.429 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.24 Å²	0 Å²	0 Å²
2-	-	0.35 Å²	0 Å²
3-	-	-	-0.11 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→90.54 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8025	0	2	693	8720

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.024	0.021	8304
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.831	1.93	11281
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.33	5	988
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.096	24.041	438
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.523	15	1383
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.09	15	57
X-RAY DIFFRACTION	r_chiral_restr	0.026	0.2	1161
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.021	6506
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.163	1.5	4930
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.87	2	7949
X-RAY DIFFRACTION	r_scbond_it	3.21	3	3374
X-RAY DIFFRACTION	r_scangle_it	4.739	4.5	3332
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.9→1.949 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.3	267	-
R_work	0.297	4990	-
obs	-	-	86.52 %

Refinement TLS params.

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

ID	L11 (°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)
1	0.6495	0.2094	-0.1121	0.4292	-0.1204	1.2266	-0.0591	0.1434	0.0087	-0.0638	0.0887	0.1235	-0.0405	-0.2072	-0.0296	0.1007	-0.0191	-0.0381	0.0635	0.0093	0.1685	-27.953	8.39	-22.998
2	9.3378	8.1977	-6.5177	7.6676	-6.8979	7.4953	0.5651	-0.6647	0.1571	0.5576	-0.8787	-0.0114	-0.5912	1.2587	0.3136	0.2563	-0.1732	-0.0933	0.6044	0.1058	0.2791	4.692	8.882	2.624
3	0.9221	0.0811	0.1845	0.4299	-0.4413	1.1848	-0.0193	0.0291	0.0291	0.0351	-0.0246	0.026	-0.2243	0.1416	0.0439	0.1507	-0.0414	-0.0264	0.0467	-0.001	0.1527	-13.083	14.796	-15.286
4	0.9382	0.456	0.0471	0.432	-0.0657	1.0496	0.0231	0.0334	-0.0243	0.0375	-0.0568	-0.044	-0.2379	0.2374	0.0338	0.2043	-0.0908	-0.0481	0.0774	0.0317	0.1304	-6.156	20.608	-18.368
5	1.0026	-0.1517	0.4183	0.5893	-0.653	2.0431	-0.0124	0.026	-0.0428	-0.0626	-0.1021	-0.0499	-0.0041	0.2403	0.1145	0.1047	-0.0044	-0.004	0.0788	0.0142	0.1467	-6.779	5.243	-16.617
6	5.5272	0.9409	1.8634	1.0949	0.4032	2.4293	-0.0447	0.1526	-0.0883	-0.1049	-0.0072	0.0466	-0.0849	0.0221	0.052	0.1573	-0.0549	-0.0288	0.0942	0.0227	0.1101	-9.548	13.425	-36.108
7	1.7624	1.0371	0.2942	0.7259	0.0573	1.089	-0.1167	0.0774	-0.01	-0.1061	-0.0687	-0.0527	-0.0403	0.4345	0.1854	0.1088	-0.0094	-0.0066	0.2423	0.0506	0.1526	4.044	4.777	-24.251
8	0.6317	0.0658	-0.0311	0.6546	0.0454	1.2423	0.0417	0.0201	0.0432	-0.0506	-0.0878	-0.1955	-0.173	0.4579	0.0461	0.1313	-0.141	-0.0214	0.2663	0.0656	0.1573	12.087	19.292	-28.071
9	0.9102	0.3016	-0.0965	1.0641	0.2647	0.2351	0.0257	-0.0207	0.0401	-0.0582	0.0194	-0.1379	-0.2646	0.1518	-0.0451	0.4577	-0.2595	-0.0397	0.1682	0.0372	0.1555	1.985	35.042	-21.562
10	9.2847	-3.5331	0.1587	7.4626	0.9001	2.5356	-0.0299	-0.2501	-0.1962	0.4923	-0.0542	-0.815	-0.2206	0.8409	0.0841	0.1236	-0.1927	-0.0965	0.4484	0.1273	0.2566	20.302	17.913	-9.368
11	10.4571	7.492	1.7162	6.4858	0.6912	0.7643	0.1436	-0.1962	0.5895	0.4606	-0.3474	0.3368	-0.3175	0.2064	0.2039	0.4905	-0.2717	-0.071	0.2376	0.0212	0.1563	-1.707	30.011	0.592
12	0.9584	-0.2391	0.0102	1.4309	-1.1419	2.7592	0.0366	-0.0887	0.1259	0.367	-0.093	0.0895	-0.7896	0.2426	0.0564	0.3335	-0.0855	-0.0314	0.0316	-0.012	0.1679	-14.098	26.534	-5.229
13	1.3951	0.0075	-0.3202	0.4236	-0.4214	2.8419	0.0192	0.0881	0.2857	0.0382	0.0246	0.1292	-0.6546	0.1075	-0.0438	0.3973	-0.0333	-0.0498	0.0176	0.0224	0.2671	-19.894	32.971	-18.376
14	3.5355	2.2436	0.4681	2.1598	0.2634	1.4384	0.0029	-0.0791	0.0193	0.0123	-0.0129	0.0269	-0.0311	-0.2119	0.0101	0.131	0.0244	-0.0123	0.0505	-0.006	0.1544	-29.46	6.334	-4.182
15	9.7067	-2.7559	3.2205	2.831	-0.3449	4.8671	-0.1707	-0.4087	-0.4059	0.1998	0.2315	0.6013	0.5433	-0.9652	-0.0608	0.1339	-0.1569	0.023	0.3443	0.0491	0.2691	-50.328	-5.688	-8.682
16	3.0458	2.1291	0.1953	1.9776	-0.0607	2.6734	-0.0931	0.1356	0.2416	-0.0876	0.2174	0.331	-0.0801	-0.814	-0.1243	0.0533	0.0175	-0.0433	0.2746	0.0785	0.2325	-46.945	8.355	-19.509
17	0.9973	0.5488	0.0107	0.7529	-0.3544	1.4437	-0.081	0.0977	0.2041	-0.0088	0.1387	0.236	-0.2156	-0.4308	-0.0577	0.1191	0.0629	-0.0324	0.1408	0.0346	0.2089	-37.905	16.092	-19.115
18	2.0961	1.9448	0.3581	3.2984	0.1531	1.7268	0.0551	-0.0315	0.147	0.1773	0.0784	0.2603	-0.218	-0.6083	-0.1335	0.0971	0.1101	0.0269	0.2371	0.0243	0.2049	-44.784	12.552	-6.458
19	3.8522	1.0461	3.3378	2.8084	0.1826	6.0374	-0.1554	-0.2662	0.5602	0.4234	0.1588	0.6128	-1.2227	-0.5662	-0.0035	0.5881	0.2399	0.044	0.118	-0.0216	0.5062	-35.444	36.483	-10.345
20	8.0519	5.8454	-1.203	9.6704	-0.0571	3.6859	-0.0858	0.1031	0.5617	0.3706	0.1516	0.5886	-0.2405	-0.8872	-0.0658	0.1221	0.1342	-0.0439	0.3256	0.0839	0.3345	-53.021	20.605	-18.181
21	2.8478	-1.1833	0.5179	5.3705	-2.081	3.0657	-0.0499	0.0766	0.5612	0.1433	-0.1294	-0.4793	-0.7663	0.6357	0.1793	0.3077	-0.2825	-0.0523	0.2674	0.0693	0.3388	19.185	36.472	-32.841
22	0.9025	-1.0611	1.6576	4.5697	-5.9917	7.9649	-0.3173	0.0815	0.6271	-0.0775	-0.0484	-0.1065	-0.0382	0.09	0.3656	0.7654	-0.6379	-0.071	0.8906	-0.0076	0.6978	24.654	34.426	-27.822
23	2.9002	0.2265	-0.458	3.5996	-0.7745	4.3201	-0.1178	0.2289	0.2801	-0.2812	-0.0835	-0.6868	-0.0542	0.7455	0.2013	0.2219	-0.255	0.0435	0.4366	0.0673	0.3733	25.633	28.845	-34.722
24	13.5985	-5.4194	0.4331	8.6919	0.7188	0.1821	-0.1423	0.6873	0.5588	-0.5088	0.0479	-0.2167	-0.1294	0.2128	0.0943	0.4051	-0.2655	0.078	0.5352	0.2208	0.2616	23.219	38.261	-44.258
25	9.5125	-1.8803	-1.73	4.5793	-0.3965	4.5704	-0.0351	0.391	-0.1139	-0.2557	-0.0678	-0.3659	-0.4654	0.698	0.1029	0.3263	-0.3036	-0.0171	0.34	0.0667	0.2035	19.563	35.044	-40.159
26	1.9213	0.0195	0.9213	1.7438	-0.576	0.6455	0.0004	0.4979	-0.0007	-0.4413	-0.104	-0.2655	0.1719	0.2979	0.1035	0.217	0.0869	0.0879	0.2405	0.0338	0.1523	-1.71	-4.334	-29.756
27	2.8529	1.9253	0.5326	5.3015	1.5018	6.9064	-0.1219	-0.0642	-0.3315	-0.2014	-0.1258	-0.0271	0.7379	0.2185	0.2477	0.2257	0.0662	0.0607	0.0604	0.0082	0.1408	-9.667	-16.348	-18.435
28	2.3154	0.5803	-0.0786	2.3624	1.3296	3.803	-0.1034	0.1704	-0.2003	-0.1121	0.0637	-0.0791	0.2765	0.4971	0.0396	0.1832	0.062	0.0365	0.1261	0.02	0.1414	-2.625	-9.32	-22.224
29	2.2843	-0.4985	-1.0334	1.8328	-2.1383	7.5968	-0.1868	0.0858	-0.1216	-0.0856	0.1557	0.1552	0.7629	-0.1927	0.0311	0.2114	-0.0296	0.0137	0.0364	-0.0171	0.1756	-17.165	-15.789	-14.424
30	1.4063	0.3758	-1.4194	1.9438	-0.9758	5.0745	-0.0664	0.1786	-0.049	-0.2177	0.0766	0.1609	0.203	-0.2365	-0.0102	0.1303	0.0105	-0.0101	0.0998	-0.0064	0.1754	-16.527	-6.459	-23.826

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 75
2	X-RAY DIFFRACTION	2	A	76 - 85
3	X-RAY DIFFRACTION	3	A	86 - 146
4	X-RAY DIFFRACTION	4	A	147 - 200
5	X-RAY DIFFRACTION	5	A	201 - 242
6	X-RAY DIFFRACTION	6	A	243 - 271
7	X-RAY DIFFRACTION	7	A	272 - 308
8	X-RAY DIFFRACTION	8	A	309 - 438
9	X-RAY DIFFRACTION	9	A	439 - 478
10	X-RAY DIFFRACTION	10	A	479 - 492
11	X-RAY DIFFRACTION	11	B	2 - 18
12	X-RAY DIFFRACTION	12	B	19 - 39
13	X-RAY DIFFRACTION	13	B	40 - 76
14	X-RAY DIFFRACTION	14	B	77 - 99
15	X-RAY DIFFRACTION	15	B	100 - 112
16	X-RAY DIFFRACTION	16	B	113 - 131
17	X-RAY DIFFRACTION	17	B	132 - 227
18	X-RAY DIFFRACTION	18	B	228 - 265
19	X-RAY DIFFRACTION	19	B	266 - 291
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